New GPCAPanel button : output pairwise alignments (pasimap only)

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 614af46..56a0476 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -315,6 +315,8 @@ label.labels = Labels
 label.output_values = Output Values...
 label.output_points = Output points...
 label.output_transformed_points = Output transformed points
+label.output_alignment = Output pairwise alignments
+label.pairwise_alignment_for_params = Pairwise alignments for {0}
 label.input_data = Input Data...
 label.nucleotide_matrix = Nucleotide matrix
 label.protein_matrix = Protein matrix

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 269d581..ab382bc 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -278,6 +278,8 @@ label.labels = Etiquetas
 label.output_values = Valores de salida...
 label.output_points = Puntos de salida...
 label.output_transformed_points = Puntos de salida transformados
+label.output_alignment = Alineaciones de pares de salida
+label.pairwise_alignment_for_params = Alineaciiones por pares para {0}
 label.input_data = Datos de entrada...
 label.nucleotide_matrix = Matriz nucleotídica
 label.protein_matrix = Matriz proteica

diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index ca49dc8..fae7e2a 100755 (executable)
--- a/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@ -57,6 +57,8 @@ public class PaSiMap implements Runnable
   /*
    * outputs
    */
+  private PairwiseAlignPanel alignment;
+
   private MatrixI pairwiseScores;
 
   private MatrixI eigenMatrix;
@@ -202,7 +204,7 @@ public class PaSiMap implements Runnable
   {
     try
     {
-      PairwiseAlignPanel alignment = new PairwiseAlignPanel(seqs, true, 100, 5);
+      alignment = new PairwiseAlignPanel(seqs, true, 100, 5);
       float[][] scores = alignment.getAlignmentScores();       //bigger index first -- eg scores[14][13]
 
       Hashtable<SequenceI, Integer> connectivity = seqs.calculateConnectivity(scores, dim);
@@ -297,4 +299,14 @@ public class PaSiMap implements Runnable
   {
     eigenMatrix = m;
   }
+
+  public PairwiseAlignPanel getAlignments()
+  {
+    return alignment;
+  }
+
+  public String getAlignmentOutput()
+  {
+    return alignment.getAlignmentOutput();
+  }
 }

diff --git a/src/jalview/gui/PaSiMapPanel.java b/src/jalview/gui/PaSiMapPanel.java
index cd1dd5a..f2445dc 100644 (file)
--- a/src/jalview/gui/PaSiMapPanel.java
+++ b/src/jalview/gui/PaSiMapPanel.java
@@ -564,6 +564,29 @@ public class PaSiMapPanel extends GPCAPanel
   /*
    * (non-Javadoc)
    * 
+   * @see
+   * jalview.jbgui.GPCAPanel#outputAlignment_actionPerformed(java.awt.event
+   * .ActionEvent)
+   */
+  @Override
+  protected void outputAlignment_actionPerformed()
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    try
+    {
+      cap.setText(getPasimapModel().getAlignmentOutput());
+      Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+       "label.pairwise_alignment_for_params", new String[] { this.getTitle() }), 500, 500);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("exporting pairwise alignments", oom);
+      cap.dispose();
+    }
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
   @Override

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index a499365..a84c449 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -55,6 +55,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   Vector<SequenceI> sequences;
 
+  private String alignmentOutput;
+
   /**
    * Creates a new PairwiseAlignPanel object.
    * 
@@ -71,6 +73,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     super();
     this.av = viewport;
 
+    StringBuilder sb = new StringBuilder(1024);
+
     sequences = new Vector<SequenceI>();
 
     SequenceGroup selectionGroup = viewport.getSelectionGroup();
@@ -128,6 +132,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         {
           System.out.println(DASHES);
           textarea.append(DASHES);
+         sb.append(DASHES);
         }
         first = false;
         as.printAlignment(System.out);
@@ -136,6 +141,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
+       sb.append(as.getOutput());
         sequences.add(as.getAlignedSeq1());
         sequences.add(as.getAlignedSeq2());
       }
@@ -149,6 +155,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     {
       printScoreMatrix(seqs, scores, totscore);
     }
+
+    alignmentOutput = sb.toString();
   }
 
   public float[][] getScores()
@@ -161,6 +169,11 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     return this.alignmentScores;
   }
 
+  public String getAlignmentOutput()
+  {
+    return this.alignmentOutput;
+  }
+
   /**
    * Prints a matrix of seqi-seqj pairwise alignment scores to sysout
    * 

diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index ec5b209..db260be 100755 (executable)
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -222,6 +222,17 @@ public class GPCAPanel extends JInternalFrame
         print_actionPerformed();
       }
     });
+    JMenuItem outputAlignment = new JMenuItem();
+    outputAlignment.setText(
+      MessageManager.getString("label.output_alignment"));
+    outputAlignment.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        outputAlignment_actionPerformed();
+      }
+    });
     viewMenu.setText(MessageManager.getString("action.view"));
     viewMenu.addMenuListener(new MenuListener()
     {
@@ -300,6 +311,7 @@ public class GPCAPanel extends JInternalFrame
     fileMenu.add(originalSeqData);
     fileMenu.add(outputPoints);
     fileMenu.add(outputProjPoints);
+    fileMenu.add(outputAlignment);
     saveMenu.add(eps);
     saveMenu.add(png);
     viewMenu.add(showLabels);
@@ -319,6 +331,10 @@ public class GPCAPanel extends JInternalFrame
   {
   }
 
+  protected void outputAlignment_actionPerformed()
+  {
+  }
+
   public void makePCAImage(TYPE imageType)
   {
   }

diff --git a/src/jalview/viewmodel/PaSiMapModel.java b/src/jalview/viewmodel/PaSiMapModel.java
index 4cc831a..84cc366 100644 (file)
--- a/src/jalview/viewmodel/PaSiMapModel.java
+++ b/src/jalview/viewmodel/PaSiMapModel.java
@@ -167,6 +167,11 @@ public class PaSiMapModel
     return pasimap.getDetails();
   }
 
+  public String getAlignmentOutput()
+  {
+    return pasimap.getAlignmentOutput();
+  }
+
   public AlignmentViewport getInputData()
   {
     return inputData;