X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=e736a1103ecacb117c0c1814fd70f5b1f4a28547;hb=daa1765ab2101480a724b92a3f3e7dee662ba943;hp=28254671cd7299834066912e7b1026ced2780b06;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 2825467..e736a11 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,98 +1,195 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
-package jalview.gui;
-
-import jalview.datamodel.*;
-import jalview.jbgui.GPairwiseAlignPanel;
-import jalview.analysis.*;
-import java.awt.event.*;
-import javax.swing.*;
-import java.util.*;
-
-
-public class PairwiseAlignPanel extends GPairwiseAlignPanel
-{
-    Vector sequences = new Vector();
-    AlignViewport av;
-
-    public PairwiseAlignPanel(AlignViewport av)
-    {
-      super();
-      this.av = av;
-      Vector selsubset = new Vector();
-      for (int i=0, j=av.getSelectionGroup().getSize(); i<j; i++)
-        if (av.getAlignment().getSequences().contains(av.getSelectionGroup().getSequenceAt(i)))
-          selsubset.add(av.getSelectionGroup().getSequenceAt(i));
-      float scores[][] = new float[selsubset.size()][selsubset.size()];
-      double totscore = 0;
-      int count = selsubset.size();
-
-      int acount = 0;
-      for (int i = 1; i < count; i++)
-      {
-        for (int j = 0; j < i; j++)
-        {
-          acount++;
-          AlignSeq as = new AlignSeq( (SequenceI) selsubset.elementAt(i),
-                                     (SequenceI) selsubset.elementAt(j), "pep");
-          as.calcScoreMatrix();
-          as.traceAlignment();
-          as.printAlignment();
-          scores[i][j] = (float) as.getMaxScore() /
-              (float) as.getASeq1().length;
-          totscore = totscore + scores[i][j];
-
-          textarea.append(as.getOutput());
-          sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));
-          sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));
-        }
-      }
-      if (count > 2)
-      {
-        System.out.println("Pairwise alignment scaled similarity score matrix\n");
-        for (int i = 0; i < count;i++)
-          jalview.util.Format.print(System.out, "%s \n", (""+i)+" "+((SequenceI) selsubset.elementAt(i)).getName());
-        System.out.println("\n");
-        for (int i = 0; i < count;i++)
-          for (int j = 0; j < i; j++)
-            jalview.util.Format.print(System.out,"%7.3f",scores[i][j]/totscore);
-        System.out.println("\n");
-
-      }
-    }
-
-
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
-  {
-
-      Sequence [] seq = new Sequence[sequences.size()];
-
-      for (int i=0;i<sequences.size();i++)
-       seq[i] = (Sequence) sequences.elementAt(i);
-
-
-      AlignFrame af = new AlignFrame(new Alignment(seq));
-      Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
-                               AlignFrame.NEW_WINDOW_WIDTH,
-                               AlignFrame.NEW_WINDOW_HEIGHT);
-
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AlignSeq;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPairwiseAlignPanel;
+import jalview.util.MessageManager;
+
+import java.awt.event.ActionEvent;
+import java.util.Vector;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class PairwiseAlignPanel extends GPairwiseAlignPanel
+{
+
+  private static final String DASHES = "---------------------\n";
+
+  AlignViewportI av;
+
+  Vector<SequenceI> sequences;
+
+  /**
+   * Creates a new PairwiseAlignPanel object.
+   * 
+   * @param viewport
+   */
+  public PairwiseAlignPanel(AlignViewportI viewport)
+  {
+    super();
+    this.av = viewport;
+
+    sequences = new Vector<>();
+
+    SequenceGroup selectionGroup = viewport.getSelectionGroup();
+    boolean isSelection = selectionGroup != null
+            && selectionGroup.getSize() > 0;
+    AlignmentView view = viewport.getAlignmentView(isSelection);
+    // String[] seqStrings = viewport.getViewAsString(true);
+    String[] seqStrings = view.getSequenceStrings(viewport
+            .getGapCharacter());
+
+    SequenceI[] seqs;
+    if (isSelection)
+    {
+      seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport
+              .getGapCharacter())[0];
+    }
+    else
+    {
+      seqs = av.getAlignment().getSequencesArray();
+    }
+
+    String type = (viewport.getAlignment().isNucleotide()) ? AlignSeq.DNA
+            : AlignSeq.PEP;
+
+    float[][] scores = new float[seqs.length][seqs.length];
+    double totscore = 0D;
+    int count = seqs.length;
+    boolean first = true;
+
+    for (int i = 1; i < count; i++)
+    {
+      for (int j = 0; j < i; j++)
+      {
+        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
+                seqStrings[j], type);
+
+        if (as.s1str.length() == 0 || as.s2str.length() == 0)
+        {
+          continue;
+        }
+
+        as.calcScoreMatrix();
+        as.traceAlignment();
+
+        if (!first)
+        {
+          System.out.println(DASHES);
+          textarea.append(DASHES);
+        }
+        first = false;
+        as.printAlignment(System.out);
+        scores[i][j] = as.getMaxScore()
+                / as.getASeq1().length;
+        totscore = totscore + scores[i][j];
+
+        textarea.append(as.getOutput());
+        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq2());
+      }
+    }
+
+    if (count > 2)
+    {
+      printScoreMatrix(seqs, scores, totscore);
+    }
+  }
+
+  /**
+   * Prints a matrix of seqi-seqj pairwise alignment scores to sysout
+   * 
+   * @param seqs
+   * @param scores
+   * @param totscore
+   */
+  protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,
+          double totscore)
+  {
+    System.out
+            .println("Pairwise alignment scaled similarity score matrix\n");
+
+    for (int i = 0; i < seqs.length; i++)
+    {
+      System.out.println(String.format("%3d %s", i + 1,
+              seqs[i].getDisplayId(true)));
+    }
+
+    /*
+     * table heading columns for sequences 1, 2, 3...
+     */
+    System.out.print("\n ");
+    for (int i = 0; i < seqs.length; i++)
+    {
+      System.out.print(String.format("%7d", i + 1));
+    }
+    System.out.println();
+
+    for (int i = 0; i < seqs.length; i++)
+    {
+      System.out.print(String.format("%3d", i + 1));
+      for (int j = 0; j < i; j++)
+      {
+        /*
+         * as a fraction of tot score, outputs are 0 <= score <= 1
+         */
+        System.out.print(String.format("%7.3f", scores[i][j] / totscore));
+      }
+      System.out.println();
+    }
+
+    System.out.println("\n");
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  @Override
+  protected void viewInEditorButton_actionPerformed(ActionEvent e)
+  {
+    SequenceI[] seq = new SequenceI[sequences.size()];
+
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      seq[i] = sequences.elementAt(i);
+    }
+
+    AlignFrame af = new AlignFrame(new Alignment(seq),
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+    Desktop.addInternalFrame(af,
+            MessageManager.getString("label.pairwise_aligned_sequences"),
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+  }
+}