Implement MSA, scoring and counting the connections

[jalview.git] / src / jalview / gui / PaSiMapPanel.java

diff --git a/src/jalview/gui/PaSiMapPanel.java b/src/jalview/gui/PaSiMapPanel.java
index e394781..62a0c80 100644 (file)
--- a/src/jalview/gui/PaSiMapPanel.java
+++ b/src/jalview/gui/PaSiMapPanel.java
@@ -109,6 +109,7 @@ public class PaSiMapPanel extends GPCAPanel
 
     boolean selected = av.getSelectionGroup() != null
             && av.getSelectionGroup().getSize() > 0;
+    //&! do i need seqstrings?
     AlignmentView seqstrings = av.getAlignmentView(selected);
     SequenceI[] seqs;
     if (!selected)
@@ -123,7 +124,9 @@ public class PaSiMapPanel extends GPCAPanel
     ScoreModelI scoreModel = ScoreModels.getInstance()
             .getScoreModel(modelName, ap);
     setPasimapModel(
-            new PaSiMapModel(seqstrings, seqs, nucleotide, scoreModel, params));
+    //&!
+            //new PaSiMapModel(seqstrings, seqs, nucleotide, scoreModel, params));
+            new PaSiMapModel(av, seqs, nucleotide, scoreModel, params));
     PaintRefresher.Register(this, av.getSequenceSetId());
 
     setRotatableCanvas(new RotatableCanvas(alignPanel));
@@ -318,7 +321,7 @@ public class PaSiMapPanel extends GPCAPanel
     }
 
     Object[] alAndColsel = getPasimapModel().getInputData()
-            .getAlignmentAndHiddenColumns(gc);
+            .getAlignmentView(false).getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
@@ -712,7 +715,9 @@ public class PaSiMapPanel extends GPCAPanel
    * 
    * @param data
    */
-  public void setInputData(AlignmentView data)
+  //public void setInputData(AlignmentView data)
+  //&! viewport or panel?
+  public void setInputData(AlignmentViewport data)
   {
     getPasimapModel().setInputData(data);
     originalSeqData.setVisible(data != null);