X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=2e1a4e0251b169ff68777dbcd96b75fcc2984d90;hb=621a628afc1f6ee7a2778b9d0ae2729b88fe5bfd;hp=a92517c3b0f09afcee0673d4e3be235589e189e8;hpb=99f3f01792321efb671ac7ad946efffc3a3319a4;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a92517c..2e1a4e0 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -61,8 +61,9 @@ public class AlignViewport
     SequenceGroup selectionGroup;
     int charHeight;
     int charWidth;
+    boolean validCharWidth;
     int wrappedWidth;
-    Font font = new Font("SansSerif", Font.PLAIN, 10);
+    Font font;
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
     int threshold;
@@ -86,6 +87,7 @@ public class AlignViewport
     AlignmentAnnotation consensus;
     AlignmentAnnotation conservation;
     AlignmentAnnotation quality;
+    boolean autoCalculateConsensus = true;
 
     /** DOCUMENT ME!! */
     public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
@@ -99,6 +101,8 @@ public class AlignViewport
 
     boolean antiAlias = false;
 
+    boolean padGaps = false;
+
 
     public AlignViewport(AlignmentI al, boolean dataset)
     {
@@ -133,6 +137,10 @@ public class AlignViewport
       showQuality = Cache.getDefault("SHOW_QUALITY", true);
       showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
 
+      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+      padGaps = Cache.getDefault("PAD_GAPS", false);
+
        String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
        String fontSize = Cache.getDefault("FONT_SIZE", "10");
@@ -310,12 +318,19 @@ public class AlignViewport
       }
       catch (OutOfMemoryError error)
       {
-        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-            "Out of memory calculating conservation!!"
-            +
-            "\nSee help files for increasing Java Virtual Machine memory."
-            , "Out of memory",
-            javax.swing.JOptionPane.WARNING_MESSAGE);
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory calculating conservation!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+
         System.out.println("Conservation calculation: " + error);
         System.gc();
 
@@ -395,12 +410,20 @@ public class AlignViewport
 
       }catch(OutOfMemoryError error)
       {
-        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-            "Out of memory calculating consensus!!"
-            +
-            "\nSee help files for increasing Java Virtual Machine memory."
-            , "Out of memory",
-            javax.swing.JOptionPane.WARNING_MESSAGE);
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory calc45ulating consensus!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+
+
         System.out.println("Consensus calculation: " + error);
         System.gc();
       }
@@ -602,6 +625,7 @@ public class AlignViewport
         java.awt.FontMetrics fm = c.getFontMetrics(font);
         setCharHeight(fm.getHeight());
         setCharWidth(fm.charWidth('M'));
+        validCharWidth = true;
     }
 
     /**
@@ -1109,8 +1133,116 @@ public class AlignViewport
         hasHiddenRows = false;
     }
 
+    public void showAllHiddenSeqs()
+    {
+      alignment.getHiddenSequences().showAll();
+      hasHiddenRows = false;
+    }
+
     public int adjustForHiddenSeqs(int alignmentIndex)
     {
       return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
     }
+
+    /**
+     * This method returns the a new SequenceI [] with
+     * the selection sequence and start and end points adjusted
+     * @return String[]
+     */
+    public SequenceI[] getSelectionAsNewSequence()
+    {
+      SequenceI[] sequences;
+
+      if (selectionGroup == null)
+        sequences = alignment.getSequencesArray();
+      else
+        sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+
+      return sequences;
+    }
+
+
+    /**
+     * This method returns the visible selected area as text, as
+     * seen on the GUI, ie if columns are hidden they will not
+     * be returned in the result.
+     * Use this for calculating trees, PCA, redundancy etc on views
+     * which contain hidden columns.
+     * @return String[]
+     */
+    public String [] getSelectionAsString()
+    {
+      String [] selection = null;
+      SequenceI [] seqs= null;
+      int i, iSize;
+      int start = 0, end = 0;
+      if(selectionGroup!=null)
+      {
+        iSize = selectionGroup.getSize(false);
+        seqs = selectionGroup.getSequencesInOrder(alignment);
+        start = selectionGroup.getStartRes();
+        end = selectionGroup.getEndRes()+1;
+      }
+      else
+      {
+        iSize = alignment.getHeight();
+        seqs = alignment.getSequencesArray();
+        end = alignment.getWidth();
+      }
+
+      selection = new String[iSize];
+
+
+      for(i=0; i<iSize; i++)
+      {
+        if (hasHiddenColumns)
+        {
+             StringBuffer visibleSeq = new StringBuffer();
+             Vector regions = colSel.getHiddenColumns();
+
+             int blockStart = start, blockEnd=end;
+             int [] region;
+             int hideStart, hideEnd;
+
+             for (int j = 0; j < regions.size(); j++)
+             {
+               region = (int[]) regions.elementAt(j);
+               hideStart = region[0];
+               hideEnd = region[1];
+
+               if(hideStart < start)
+               {
+                 continue;
+               }
+
+               blockStart = Math.min(blockStart, hideEnd+1);
+               blockEnd = Math.min(blockEnd, hideStart);
+
+               if(blockStart>blockEnd)
+               {
+                  break;
+               }
+
+
+               visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+               blockStart = hideEnd+1;
+               blockEnd = end;
+             }
+
+             if(end>blockStart)
+               visibleSeq.append(seqs[i].getSequence(blockStart, end));
+
+             selection[i] = visibleSeq.toString();
+        }
+        else
+        {
+          selection[i] = seqs[i].getSequence(start, end);
+        }
+
+    //    System.out.println(seqs[i].getName()+"\t"+ selection[i]);
+      }
+
+      return selection;
+    }
 }