Class |
Line # |
Actions |
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PairwiseAlignPanel | 38 | 53 | 17 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.appletgui; | |
22 | ||
23 | import jalview.analysis.AlignSeq; | |
24 | import jalview.datamodel.Alignment; | |
25 | import jalview.datamodel.Sequence; | |
26 | import jalview.datamodel.SequenceI; | |
27 | import jalview.util.MessageManager; | |
28 | ||
29 | import java.awt.BorderLayout; | |
30 | import java.awt.Button; | |
31 | import java.awt.Panel; | |
32 | import java.awt.ScrollPane; | |
33 | import java.awt.TextArea; | |
34 | import java.awt.event.ActionEvent; | |
35 | import java.awt.event.ActionListener; | |
36 | import java.util.Vector; | |
37 | ||
38 | public class PairwiseAlignPanel extends Panel implements ActionListener | |
39 | { | |
40 | Vector sequences = new Vector(); | |
41 | ||
42 | AlignmentPanel ap; | |
43 | ||
44 | 0 | public PairwiseAlignPanel(AlignmentPanel ap) |
45 | { | |
46 | 0 | try |
47 | { | |
48 | 0 | jbInit(); |
49 | } catch (Exception e) | |
50 | { | |
51 | 0 | e.printStackTrace(); |
52 | } | |
53 | 0 | this.ap = ap; |
54 | 0 | sequences = new Vector(); |
55 | ||
56 | 0 | SequenceI[] seqs; |
57 | 0 | String[] seqStrings = ap.av.getViewAsString(true); |
58 | ||
59 | 0 | if (ap.av.getSelectionGroup() == null) |
60 | { | |
61 | 0 | seqs = ap.av.getAlignment().getSequencesArray(); |
62 | } | |
63 | else | |
64 | { | |
65 | 0 | seqs = ap.av.getSelectionGroup() |
66 | .getSequencesInOrder(ap.av.getAlignment()); | |
67 | } | |
68 | ||
69 | 0 | float scores[][] = new float[seqs.length][seqs.length]; |
70 | 0 | double totscore = 0; |
71 | 0 | int count = ap.av.getSelectionGroup().getSize(); |
72 | 0 | String type = (ap.av.getAlignment().isNucleotide()) ? AlignSeq.DNA |
73 | : AlignSeq.PEP; | |
74 | 0 | Sequence seq; |
75 | ||
76 | 0 | for (int i = 1; i < count; i++) |
77 | { | |
78 | 0 | for (int j = 0; j < i; j++) |
79 | { | |
80 | ||
81 | 0 | AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j], |
82 | seqStrings[j], type); | |
83 | ||
84 | 0 | if (as.s1str.length() == 0 || as.s2str.length() == 0) |
85 | { | |
86 | 0 | continue; |
87 | } | |
88 | ||
89 | 0 | as.calcScoreMatrix(); |
90 | 0 | as.traceAlignment(); |
91 | ||
92 | 0 | as.printAlignment(System.out); |
93 | 0 | scores[i][j] = (float) as.getMaxScore() |
94 | / (float) as.getASeq1().length; | |
95 | 0 | totscore = totscore + scores[i][j]; |
96 | ||
97 | 0 | textarea.append(as.getOutput()); |
98 | 0 | sequences.add(as.getAlignedSeq1()); |
99 | 0 | sequences.add(as.getAlignedSeq1()); |
100 | } | |
101 | } | |
102 | ||
103 | 0 | if (count > 2) |
104 | { | |
105 | 0 | jalview.bin.Console.outPrintln( |
106 | "Pairwise alignment scaled similarity score matrix\n"); | |
107 | ||
108 | 0 | for (int i = 0; i < count; i++) |
109 | { | |
110 | 0 | jalview.util.Format.print(System.out, "%s \n", |
111 | ("" + i) + " " + seqs[i].getName()); | |
112 | } | |
113 | ||
114 | 0 | jalview.bin.Console.outPrintln("\n"); |
115 | ||
116 | 0 | for (int i = 0; i < count; i++) |
117 | { | |
118 | 0 | for (int j = 0; j < i; j++) |
119 | { | |
120 | 0 | jalview.util.Format.print(System.out, "%7.3f", |
121 | scores[i][j] / totscore); | |
122 | } | |
123 | } | |
124 | ||
125 | 0 | jalview.bin.Console.outPrintln("\n"); |
126 | } | |
127 | } | |
128 | ||
129 | 0 | public void actionPerformed(ActionEvent evt) |
130 | { | |
131 | 0 | if (evt.getSource() == viewInEditorButton) |
132 | { | |
133 | 0 | viewInEditorButton_actionPerformed(); |
134 | } | |
135 | } | |
136 | ||
137 | 0 | protected void viewInEditorButton_actionPerformed() |
138 | { | |
139 | ||
140 | 0 | Sequence[] seq = new Sequence[sequences.size()]; |
141 | ||
142 | 0 | for (int i = 0; i < sequences.size(); i++) |
143 | { | |
144 | 0 | seq[i] = (Sequence) sequences.elementAt(i); |
145 | } | |
146 | ||
147 | 0 | new AlignFrame(new Alignment(seq), ap.av.applet, |
148 | "Pairwise Aligned Sequences", false); | |
149 | ||
150 | } | |
151 | ||
152 | protected ScrollPane scrollPane = new ScrollPane(); | |
153 | ||
154 | protected TextArea textarea = new TextArea(); | |
155 | ||
156 | protected Button viewInEditorButton = new Button(); | |
157 | ||
158 | Panel jPanel1 = new Panel(); | |
159 | ||
160 | BorderLayout borderLayout1 = new BorderLayout(); | |
161 | ||
162 | 0 | private void jbInit() throws Exception |
163 | { | |
164 | 0 | this.setLayout(borderLayout1); |
165 | 0 | textarea.setFont(new java.awt.Font("Monospaced", 0, 12)); |
166 | 0 | textarea.setText(""); |
167 | 0 | viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12)); |
168 | 0 | viewInEditorButton.setLabel( |
169 | MessageManager.getString("label.view_alignment_editor")); | |
170 | 0 | viewInEditorButton.addActionListener(this); |
171 | 0 | this.add(scrollPane, BorderLayout.CENTER); |
172 | 0 | scrollPane.add(textarea); |
173 | 0 | this.add(jPanel1, BorderLayout.SOUTH); |
174 | 0 | jPanel1.add(viewInEditorButton, null); |
175 | } | |
176 | ||
177 | } |