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package jalview.schemabinding.version2; |
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import org.exolab.castor.xml.Marshaller; |
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import org.exolab.castor.xml.Unmarshaller; |
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@version |
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| 65.2% |
Uncovered Elements: 80 (230) |
Complexity: 103 |
Complexity Density: 0.81 |
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public class JGroup implements java.io.Serializable |
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{ |
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private int _start; |
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private boolean _has_start; |
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private int _end; |
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private boolean _has_end; |
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private java.lang.String _name; |
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private java.lang.String _colour; |
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private int _consThreshold; |
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private boolean _has_consThreshold; |
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private int _pidThreshold; |
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private boolean _has_pidThreshold; |
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private int _outlineColour; |
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private boolean _has_outlineColour; |
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private boolean _displayBoxes; |
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private boolean _has_displayBoxes; |
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private boolean _displayText; |
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private boolean _has_displayText; |
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private boolean _colourText; |
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private boolean _has_colourText; |
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private int _textCol1; |
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private boolean _has_textCol1; |
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private int _textCol2; |
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private boolean _has_textCol2; |
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private int _textColThreshold; |
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private boolean _has_textColThreshold; |
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private boolean _showUnconserved; |
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private boolean _has_showUnconserved; |
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private boolean _ignoreGapsinConsensus = true; |
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private boolean _has_ignoreGapsinConsensus; |
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private boolean _showConsensusHistogram = true; |
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private boolean _has_showConsensusHistogram; |
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private boolean _showSequenceLogo = false; |
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private boolean _has_showSequenceLogo; |
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private boolean _normaliseSequenceLogo = false; |
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private boolean _has_normaliseSequenceLogo; |
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private java.lang.String _id; |
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private java.util.Vector _seqList; |
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private jalview.schemabinding.version2.AnnotationColours _annotationColours; |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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public JGroup()... |
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{ |
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super(); |
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this._seqList = new java.util.Vector(); |
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} |
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@param |
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@throws |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public void addSeq(final java.lang.String vSeq)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._seqList.addElement(vSeq); |
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} |
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@param |
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@param |
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@throws |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void addSeq(final int index, final java.lang.String vSeq)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._seqList.add(index, vSeq); |
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} |
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256 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteColourText()... |
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{ |
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this._has_colourText = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteConsThreshold()... |
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{ |
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this._has_consThreshold = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteDisplayBoxes()... |
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{ |
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this._has_displayBoxes = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteDisplayText()... |
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{ |
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this._has_displayText = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteEnd()... |
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{ |
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this._has_end = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteIgnoreGapsinConsensus()... |
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{ |
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this._has_ignoreGapsinConsensus = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteNormaliseSequenceLogo()... |
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{ |
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this._has_normaliseSequenceLogo = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteOutlineColour()... |
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{ |
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this._has_outlineColour = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deletePidThreshold()... |
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{ |
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this._has_pidThreshold = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteShowConsensusHistogram()... |
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{ |
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this._has_showConsensusHistogram = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteShowSequenceLogo()... |
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{ |
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this._has_showSequenceLogo = false; |
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} |
332 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteShowUnconserved()... |
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{ |
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this._has_showUnconserved = false; |
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} |
339 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public void deleteStart()... |
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{ |
344 |
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this._has_start = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteTextCol1()... |
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{ |
351 |
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this._has_textCol1 = false; |
352 |
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} |
353 |
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354 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public void deleteTextCol2()... |
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{ |
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this._has_textCol2 = false; |
359 |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteTextColThreshold()... |
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{ |
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this._has_textColThreshold = false; |
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} |
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@return |
372 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public java.util.Enumeration enumerateSeq()... |
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{ |
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return this._seqList.elements(); |
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} |
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@return |
382 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()... |
384 |
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{ |
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return this._annotationColours; |
386 |
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} |
387 |
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388 |
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389 |
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390 |
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391 |
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@return |
392 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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167 |
public java.lang.String getColour()... |
394 |
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{ |
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return this._colour; |
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} |
397 |
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398 |
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399 |
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400 |
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401 |
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@return |
402 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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87 |
public boolean getColourText()... |
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{ |
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return this._colourText; |
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} |
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408 |
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409 |
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411 |
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@return |
412 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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128 |
public int getConsThreshold()... |
414 |
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{ |
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return this._consThreshold; |
416 |
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} |
417 |
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418 |
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419 |
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420 |
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421 |
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@return |
422 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
423 |
87 |
public boolean getDisplayBoxes()... |
424 |
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{ |
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return this._displayBoxes; |
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} |
427 |
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428 |
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429 |
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430 |
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431 |
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@return |
432 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
433 |
87 |
public boolean getDisplayText()... |
434 |
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{ |
435 |
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return this._displayText; |
436 |
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} |
437 |
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438 |
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439 |
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440 |
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441 |
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@return |
442 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
443 |
87 |
public int getEnd()... |
444 |
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{ |
445 |
87 |
return this._end; |
446 |
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} |
447 |
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448 |
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449 |
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450 |
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451 |
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452 |
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453 |
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454 |
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@return |
455 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
456 |
123 |
public java.lang.String getId()... |
457 |
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{ |
458 |
123 |
return this._id; |
459 |
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} |
460 |
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461 |
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462 |
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463 |
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464 |
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@return |
465 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
466 |
87 |
public boolean getIgnoreGapsinConsensus()... |
467 |
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{ |
468 |
87 |
return this._ignoreGapsinConsensus; |
469 |
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} |
470 |
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471 |
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472 |
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473 |
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474 |
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@return |
475 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
476 |
87 |
public java.lang.String getName()... |
477 |
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{ |
478 |
87 |
return this._name; |
479 |
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} |
480 |
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481 |
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482 |
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483 |
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|
484 |
|
@return |
485 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
486 |
24 |
public boolean getNormaliseSequenceLogo()... |
487 |
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{ |
488 |
24 |
return this._normaliseSequenceLogo; |
489 |
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} |
490 |
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491 |
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492 |
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493 |
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|
494 |
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@return |
495 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
496 |
87 |
public int getOutlineColour()... |
497 |
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{ |
498 |
87 |
return this._outlineColour; |
499 |
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} |
500 |
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501 |
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502 |
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503 |
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|
504 |
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@return |
505 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
506 |
75 |
public int getPidThreshold()... |
507 |
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{ |
508 |
75 |
return this._pidThreshold; |
509 |
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} |
510 |
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511 |
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512 |
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513 |
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|
514 |
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@param |
515 |
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@throws |
516 |
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|
517 |
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@return |
518 |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
519 |
484 |
public java.lang.String getSeq(final int index)... |
520 |
|
throws java.lang.IndexOutOfBoundsException |
521 |
|
{ |
522 |
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|
523 |
484 |
if (index < 0 || index >= this._seqList.size()) |
524 |
|
{ |
525 |
0 |
throw new IndexOutOfBoundsException("getSeq: Index value '" + index |
526 |
|
+ "' not in range [0.." + (this._seqList.size() - 1) + "]"); |
527 |
|
} |
528 |
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|
529 |
484 |
return (java.lang.String) _seqList.get(index); |
530 |
|
} |
531 |
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|
532 |
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|
533 |
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|
534 |
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|
535 |
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|
536 |
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|
537 |
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|
538 |
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|
539 |
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@return |
540 |
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|
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
541 |
24 |
public java.lang.String[] getSeq()... |
542 |
|
{ |
543 |
24 |
java.lang.String[] array = new java.lang.String[0]; |
544 |
24 |
return (java.lang.String[]) this._seqList.toArray(array); |
545 |
|
} |
546 |
|
|
547 |
|
|
548 |
|
|
549 |
|
|
550 |
|
@return |
551 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
552 |
547 |
public int getSeqCount()... |
553 |
|
{ |
554 |
547 |
return this._seqList.size(); |
555 |
|
} |
556 |
|
|
557 |
|
|
558 |
|
|
559 |
|
|
560 |
|
@return |
561 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
562 |
24 |
public boolean getShowConsensusHistogram()... |
563 |
|
{ |
564 |
24 |
return this._showConsensusHistogram; |
565 |
|
} |
566 |
|
|
567 |
|
|
568 |
|
|
569 |
|
|
570 |
|
@return |
571 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
572 |
24 |
public boolean getShowSequenceLogo()... |
573 |
|
{ |
574 |
24 |
return this._showSequenceLogo; |
575 |
|
} |
576 |
|
|
577 |
|
|
578 |
|
|
579 |
|
|
580 |
|
@return |
581 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
582 |
24 |
public boolean getShowUnconserved()... |
583 |
|
{ |
584 |
24 |
return this._showUnconserved; |
585 |
|
} |
586 |
|
|
587 |
|
|
588 |
|
|
589 |
|
|
590 |
|
@return |
591 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
592 |
87 |
public int getStart()... |
593 |
|
{ |
594 |
87 |
return this._start; |
595 |
|
} |
596 |
|
|
597 |
|
|
598 |
|
|
599 |
|
|
600 |
|
@return |
601 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
602 |
87 |
public int getTextCol1()... |
603 |
|
{ |
604 |
87 |
return this._textCol1; |
605 |
|
} |
606 |
|
|
607 |
|
|
608 |
|
|
609 |
|
|
610 |
|
@return |
611 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
612 |
87 |
public int getTextCol2()... |
613 |
|
{ |
614 |
87 |
return this._textCol2; |
615 |
|
} |
616 |
|
|
617 |
|
|
618 |
|
|
619 |
|
|
620 |
|
@return |
621 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
622 |
87 |
public int getTextColThreshold()... |
623 |
|
{ |
624 |
87 |
return this._textColThreshold; |
625 |
|
} |
626 |
|
|
627 |
|
|
628 |
|
|
629 |
|
|
630 |
|
@return |
631 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
632 |
24 |
public boolean hasColourText()... |
633 |
|
{ |
634 |
24 |
return this._has_colourText; |
635 |
|
} |
636 |
|
|
637 |
|
|
638 |
|
|
639 |
|
|
640 |
|
@return |
641 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
642 |
24 |
public boolean hasConsThreshold()... |
643 |
|
{ |
644 |
24 |
return this._has_consThreshold; |
645 |
|
} |
646 |
|
|
647 |
|
|
648 |
|
|
649 |
|
|
650 |
|
@return |
651 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
652 |
24 |
public boolean hasDisplayBoxes()... |
653 |
|
{ |
654 |
24 |
return this._has_displayBoxes; |
655 |
|
} |
656 |
|
|
657 |
|
|
658 |
|
|
659 |
|
|
660 |
|
@return |
661 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
662 |
24 |
public boolean hasDisplayText()... |
663 |
|
{ |
664 |
24 |
return this._has_displayText; |
665 |
|
} |
666 |
|
|
667 |
|
|
668 |
|
|
669 |
|
|
670 |
|
@return |
671 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
672 |
24 |
public boolean hasEnd()... |
673 |
|
{ |
674 |
24 |
return this._has_end; |
675 |
|
} |
676 |
|
|
677 |
|
|
678 |
|
|
679 |
|
|
680 |
|
@return |
681 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
682 |
87 |
public boolean hasIgnoreGapsinConsensus()... |
683 |
|
{ |
684 |
87 |
return this._has_ignoreGapsinConsensus; |
685 |
|
} |
686 |
|
|
687 |
|
|
688 |
|
|
689 |
|
|
690 |
|
@return |
691 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
692 |
87 |
public boolean hasNormaliseSequenceLogo()... |
693 |
|
{ |
694 |
87 |
return this._has_normaliseSequenceLogo; |
695 |
|
} |
696 |
|
|
697 |
|
|
698 |
|
|
699 |
|
|
700 |
|
@return |
701 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
702 |
24 |
public boolean hasOutlineColour()... |
703 |
|
{ |
704 |
24 |
return this._has_outlineColour; |
705 |
|
} |
706 |
|
|
707 |
|
|
708 |
|
|
709 |
|
|
710 |
|
@return |
711 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
712 |
24 |
public boolean hasPidThreshold()... |
713 |
|
{ |
714 |
24 |
return this._has_pidThreshold; |
715 |
|
} |
716 |
|
|
717 |
|
|
718 |
|
|
719 |
|
|
720 |
|
@return |
721 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
722 |
87 |
public boolean hasShowConsensusHistogram()... |
723 |
|
{ |
724 |
87 |
return this._has_showConsensusHistogram; |
725 |
|
} |
726 |
|
|
727 |
|
|
728 |
|
|
729 |
|
|
730 |
|
@return |
731 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
732 |
87 |
public boolean hasShowSequenceLogo()... |
733 |
|
{ |
734 |
87 |
return this._has_showSequenceLogo; |
735 |
|
} |
736 |
|
|
737 |
|
|
738 |
|
|
739 |
|
|
740 |
|
@return |
741 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
742 |
87 |
public boolean hasShowUnconserved()... |
743 |
|
{ |
744 |
87 |
return this._has_showUnconserved; |
745 |
|
} |
746 |
|
|
747 |
|
|
748 |
|
|
749 |
|
|
750 |
|
@return |
751 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
752 |
24 |
public boolean hasStart()... |
753 |
|
{ |
754 |
24 |
return this._has_start; |
755 |
|
} |
756 |
|
|
757 |
|
|
758 |
|
|
759 |
|
|
760 |
|
@return |
761 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
762 |
24 |
public boolean hasTextCol1()... |
763 |
|
{ |
764 |
24 |
return this._has_textCol1; |
765 |
|
} |
766 |
|
|
767 |
|
|
768 |
|
|
769 |
|
|
770 |
|
@return |
771 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
772 |
24 |
public boolean hasTextCol2()... |
773 |
|
{ |
774 |
24 |
return this._has_textCol2; |
775 |
|
} |
776 |
|
|
777 |
|
|
778 |
|
|
779 |
|
|
780 |
|
@return |
781 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
782 |
24 |
public boolean hasTextColThreshold()... |
783 |
|
{ |
784 |
24 |
return this._has_textColThreshold; |
785 |
|
} |
786 |
|
|
787 |
|
|
788 |
|
|
789 |
|
|
790 |
|
@return |
791 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
792 |
0 |
public boolean isColourText()... |
793 |
|
{ |
794 |
0 |
return this._colourText; |
795 |
|
} |
796 |
|
|
797 |
|
|
798 |
|
|
799 |
|
|
800 |
|
@return |
801 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
802 |
0 |
public boolean isDisplayBoxes()... |
803 |
|
{ |
804 |
0 |
return this._displayBoxes; |
805 |
|
} |
806 |
|
|
807 |
|
|
808 |
|
|
809 |
|
|
810 |
|
@return |
811 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
812 |
0 |
public boolean isDisplayText()... |
813 |
|
{ |
814 |
0 |
return this._displayText; |
815 |
|
} |
816 |
|
|
817 |
|
|
818 |
|
|
819 |
|
|
820 |
|
@return |
821 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
822 |
0 |
public boolean isIgnoreGapsinConsensus()... |
823 |
|
{ |
824 |
0 |
return this._ignoreGapsinConsensus; |
825 |
|
} |
826 |
|
|
827 |
|
|
828 |
|
|
829 |
|
|
830 |
|
@return |
831 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
832 |
13 |
public boolean isNormaliseSequenceLogo()... |
833 |
|
{ |
834 |
13 |
return this._normaliseSequenceLogo; |
835 |
|
} |
836 |
|
|
837 |
|
|
838 |
|
|
839 |
|
|
840 |
|
@return |
841 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
842 |
63 |
public boolean isShowConsensusHistogram()... |
843 |
|
{ |
844 |
63 |
return this._showConsensusHistogram; |
845 |
|
} |
846 |
|
|
847 |
|
|
848 |
|
|
849 |
|
|
850 |
|
@return |
851 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
852 |
63 |
public boolean isShowSequenceLogo()... |
853 |
|
{ |
854 |
63 |
return this._showSequenceLogo; |
855 |
|
} |
856 |
|
|
857 |
|
|
858 |
|
|
859 |
|
|
860 |
|
@return |
861 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
862 |
63 |
public boolean isShowUnconserved()... |
863 |
|
{ |
864 |
63 |
return this._showUnconserved; |
865 |
|
} |
866 |
|
|
867 |
|
|
868 |
|
|
869 |
|
|
870 |
|
@return |
871 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
872 |
0 |
public boolean isValid()... |
873 |
|
{ |
874 |
0 |
try |
875 |
|
{ |
876 |
0 |
validate(); |
877 |
|
} catch (org.exolab.castor.xml.ValidationException vex) |
878 |
|
{ |
879 |
0 |
return false; |
880 |
|
} |
881 |
0 |
return true; |
882 |
|
} |
883 |
|
|
884 |
|
|
885 |
|
|
886 |
|
|
887 |
|
@param |
888 |
|
@throws |
889 |
|
|
890 |
|
|
891 |
|
@throws |
892 |
|
|
893 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
894 |
0 |
public void marshal(final java.io.Writer out)... |
895 |
|
throws org.exolab.castor.xml.MarshalException, |
896 |
|
org.exolab.castor.xml.ValidationException |
897 |
|
{ |
898 |
0 |
Marshaller.marshal(this, out); |
899 |
|
} |
900 |
|
|
901 |
|
|
902 |
|
|
903 |
|
|
904 |
|
@param |
905 |
|
@throws |
906 |
|
|
907 |
|
@throws |
908 |
|
|
909 |
|
@throws |
910 |
|
|
911 |
|
|
912 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
913 |
0 |
public void marshal(final org.xml.sax.ContentHandler handler)... |
914 |
|
throws java.io.IOException, |
915 |
|
org.exolab.castor.xml.MarshalException, |
916 |
|
org.exolab.castor.xml.ValidationException |
917 |
|
{ |
918 |
0 |
Marshaller.marshal(this, handler); |
919 |
|
} |
920 |
|
|
921 |
|
|
922 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
923 |
0 |
public void removeAllSeq()... |
924 |
|
{ |
925 |
0 |
this._seqList.clear(); |
926 |
|
} |
927 |
|
|
928 |
|
|
929 |
|
|
930 |
|
|
931 |
|
@param |
932 |
|
@return |
933 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
934 |
0 |
public boolean removeSeq(final java.lang.String vSeq)... |
935 |
|
{ |
936 |
0 |
boolean removed = _seqList.remove(vSeq); |
937 |
0 |
return removed; |
938 |
|
} |
939 |
|
|
940 |
|
|
941 |
|
|
942 |
|
|
943 |
|
@param |
944 |
|
@return |
945 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
946 |
0 |
public java.lang.String removeSeqAt(final int index)... |
947 |
|
{ |
948 |
0 |
java.lang.Object obj = this._seqList.remove(index); |
949 |
0 |
return (java.lang.String) obj; |
950 |
|
} |
951 |
|
|
952 |
|
|
953 |
|
|
954 |
|
|
955 |
|
@param |
956 |
|
|
957 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
958 |
2 |
public void setAnnotationColours(... |
959 |
|
final jalview.schemabinding.version2.AnnotationColours annotationColours) |
960 |
|
{ |
961 |
2 |
this._annotationColours = annotationColours; |
962 |
|
} |
963 |
|
|
964 |
|
|
965 |
|
|
966 |
|
|
967 |
|
@param |
968 |
|
|
969 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
970 |
33 |
public void setColour(final java.lang.String colour)... |
971 |
|
{ |
972 |
33 |
this._colour = colour; |
973 |
|
} |
974 |
|
|
975 |
|
|
976 |
|
|
977 |
|
|
978 |
|
@param |
979 |
|
|
980 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
981 |
75 |
public void setColourText(final boolean colourText)... |
982 |
|
{ |
983 |
75 |
this._colourText = colourText; |
984 |
75 |
this._has_colourText = true; |
985 |
|
} |
986 |
|
|
987 |
|
|
988 |
|
|
989 |
|
|
990 |
|
@param |
991 |
|
|
992 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
993 |
3 |
public void setConsThreshold(final int consThreshold)... |
994 |
|
{ |
995 |
3 |
this._consThreshold = consThreshold; |
996 |
3 |
this._has_consThreshold = true; |
997 |
|
} |
998 |
|
|
999 |
|
|
1000 |
|
|
1001 |
|
|
1002 |
|
@param |
1003 |
|
|
1004 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1005 |
75 |
public void setDisplayBoxes(final boolean displayBoxes)... |
1006 |
|
{ |
1007 |
75 |
this._displayBoxes = displayBoxes; |
1008 |
75 |
this._has_displayBoxes = true; |
1009 |
|
} |
1010 |
|
|
1011 |
|
|
1012 |
|
|
1013 |
|
|
1014 |
|
@param |
1015 |
|
|
1016 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1017 |
75 |
public void setDisplayText(final boolean displayText)... |
1018 |
|
{ |
1019 |
75 |
this._displayText = displayText; |
1020 |
75 |
this._has_displayText = true; |
1021 |
|
} |
1022 |
|
|
1023 |
|
|
1024 |
|
|
1025 |
|
|
1026 |
|
@param |
1027 |
|
|
1028 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1029 |
75 |
public void setEnd(final int end)... |
1030 |
|
{ |
1031 |
75 |
this._end = end; |
1032 |
75 |
this._has_end = true; |
1033 |
|
} |
1034 |
|
|
1035 |
|
|
1036 |
|
|
1037 |
|
|
1038 |
|
|
1039 |
|
|
1040 |
|
@param |
1041 |
|
|
1042 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1043 |
42 |
public void setId(final java.lang.String id)... |
1044 |
|
{ |
1045 |
42 |
this._id = id; |
1046 |
|
} |
1047 |
|
|
1048 |
|
|
1049 |
|
|
1050 |
|
|
1051 |
|
@param |
1052 |
|
|
1053 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1054 |
75 |
public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)... |
1055 |
|
{ |
1056 |
75 |
this._ignoreGapsinConsensus = ignoreGapsinConsensus; |
1057 |
75 |
this._has_ignoreGapsinConsensus = true; |
1058 |
|
} |
1059 |
|
|
1060 |
|
|
1061 |
|
|
1062 |
|
|
1063 |
|
@param |
1064 |
|
|
1065 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1066 |
75 |
public void setName(final java.lang.String name)... |
1067 |
|
{ |
1068 |
75 |
this._name = name; |
1069 |
|
} |
1070 |
|
|
1071 |
|
|
1072 |
|
|
1073 |
|
|
1074 |
|
@param |
1075 |
|
|
1076 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1077 |
25 |
public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)... |
1078 |
|
{ |
1079 |
25 |
this._normaliseSequenceLogo = normaliseSequenceLogo; |
1080 |
25 |
this._has_normaliseSequenceLogo = true; |
1081 |
|
} |
1082 |
|
|
1083 |
|
|
1084 |
|
|
1085 |
|
|
1086 |
|
@param |
1087 |
|
|
1088 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1089 |
75 |
public void setOutlineColour(final int outlineColour)... |
1090 |
|
{ |
1091 |
75 |
this._outlineColour = outlineColour; |
1092 |
75 |
this._has_outlineColour = true; |
1093 |
|
} |
1094 |
|
|
1095 |
|
|
1096 |
|
|
1097 |
|
|
1098 |
|
@param |
1099 |
|
|
1100 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1101 |
33 |
public void setPidThreshold(final int pidThreshold)... |
1102 |
|
{ |
1103 |
33 |
this._pidThreshold = pidThreshold; |
1104 |
33 |
this._has_pidThreshold = true; |
1105 |
|
} |
1106 |
|
|
1107 |
|
|
1108 |
|
|
1109 |
|
|
1110 |
|
@param |
1111 |
|
@param |
1112 |
|
@throws |
1113 |
|
|
1114 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
1115 |
0 |
public void setSeq(final int index, final java.lang.String vSeq)... |
1116 |
|
throws java.lang.IndexOutOfBoundsException |
1117 |
|
{ |
1118 |
|
|
1119 |
0 |
if (index < 0 || index >= this._seqList.size()) |
1120 |
|
{ |
1121 |
0 |
throw new IndexOutOfBoundsException("setSeq: Index value '" + index |
1122 |
|
+ "' not in range [0.." + (this._seqList.size() - 1) + "]"); |
1123 |
|
} |
1124 |
|
|
1125 |
0 |
this._seqList.set(index, vSeq); |
1126 |
|
} |
1127 |
|
|
1128 |
|
|
1129 |
|
|
1130 |
|
|
1131 |
|
@param |
1132 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1133 |
0 |
public void setSeq(final java.lang.String[] vSeqArray)... |
1134 |
|
{ |
1135 |
|
|
1136 |
0 |
_seqList.clear(); |
1137 |
|
|
1138 |
0 |
for (int i = 0; i < vSeqArray.length; i++) |
1139 |
|
{ |
1140 |
0 |
this._seqList.add(vSeqArray[i]); |
1141 |
|
} |
1142 |
|
} |
1143 |
|
|
1144 |
|
|
1145 |
|
|
1146 |
|
|
1147 |
|
@param |
1148 |
|
|
1149 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1150 |
75 |
public void setShowConsensusHistogram(final boolean showConsensusHistogram)... |
1151 |
|
{ |
1152 |
75 |
this._showConsensusHistogram = showConsensusHistogram; |
1153 |
75 |
this._has_showConsensusHistogram = true; |
1154 |
|
} |
1155 |
|
|
1156 |
|
|
1157 |
|
|
1158 |
|
|
1159 |
|
@param |
1160 |
|
|
1161 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1162 |
75 |
public void setShowSequenceLogo(final boolean showSequenceLogo)... |
1163 |
|
{ |
1164 |
75 |
this._showSequenceLogo = showSequenceLogo; |
1165 |
75 |
this._has_showSequenceLogo = true; |
1166 |
|
} |
1167 |
|
|
1168 |
|
|
1169 |
|
|
1170 |
|
|
1171 |
|
@param |
1172 |
|
|
1173 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1174 |
75 |
public void setShowUnconserved(final boolean showUnconserved)... |
1175 |
|
{ |
1176 |
75 |
this._showUnconserved = showUnconserved; |
1177 |
75 |
this._has_showUnconserved = true; |
1178 |
|
} |
1179 |
|
|
1180 |
|
|
1181 |
|
|
1182 |
|
|
1183 |
|
@param |
1184 |
|
|
1185 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1186 |
75 |
public void setStart(final int start)... |
1187 |
|
{ |
1188 |
75 |
this._start = start; |
1189 |
75 |
this._has_start = true; |
1190 |
|
} |
1191 |
|
|
1192 |
|
|
1193 |
|
|
1194 |
|
|
1195 |
|
@param |
1196 |
|
|
1197 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1198 |
75 |
public void setTextCol1(final int textCol1)... |
1199 |
|
{ |
1200 |
75 |
this._textCol1 = textCol1; |
1201 |
75 |
this._has_textCol1 = true; |
1202 |
|
} |
1203 |
|
|
1204 |
|
|
1205 |
|
|
1206 |
|
|
1207 |
|
@param |
1208 |
|
|
1209 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1210 |
75 |
public void setTextCol2(final int textCol2)... |
1211 |
|
{ |
1212 |
75 |
this._textCol2 = textCol2; |
1213 |
75 |
this._has_textCol2 = true; |
1214 |
|
} |
1215 |
|
|
1216 |
|
|
1217 |
|
|
1218 |
|
|
1219 |
|
@param |
1220 |
|
|
1221 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1222 |
75 |
public void setTextColThreshold(final int textColThreshold)... |
1223 |
|
{ |
1224 |
75 |
this._textColThreshold = textColThreshold; |
1225 |
75 |
this._has_textColThreshold = true; |
1226 |
|
} |
1227 |
|
|
1228 |
|
|
1229 |
|
|
1230 |
|
|
1231 |
|
@param |
1232 |
|
@throws |
1233 |
|
|
1234 |
|
|
1235 |
|
@throws |
1236 |
|
|
1237 |
|
@return |
1238 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1239 |
0 |
public static jalview.schemabinding.version2.JGroup unmarshal(... |
1240 |
|
final java.io.Reader reader) |
1241 |
|
throws org.exolab.castor.xml.MarshalException, |
1242 |
|
org.exolab.castor.xml.ValidationException |
1243 |
|
{ |
1244 |
0 |
return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal( |
1245 |
|
jalview.schemabinding.version2.JGroup.class, reader); |
1246 |
|
} |
1247 |
|
|
1248 |
|
|
1249 |
|
|
1250 |
|
|
1251 |
|
@throws |
1252 |
|
|
1253 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1254 |
0 |
public void validate() throws org.exolab.castor.xml.ValidationException... |
1255 |
|
{ |
1256 |
0 |
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); |
1257 |
0 |
validator.validate(this); |
1258 |
|
} |
1259 |
|
|
1260 |
|
} |