X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=9d63cde5867d0e4abe881d47f7777e9260d9bf18;hb=d1055a6dd6cc9d065e9e589eae260c16cb941265;hp=b21f47e67c792ad0067c4d9903cd9ef634f4fb64;hpb=e142bcca7d3c8a10695b87f94bc724cc2f5ab165;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b21f47e..9d63cde 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,7 +1,7 @@
 package jalview.gui;
 
 import java.awt.*;
-import jalview.io.*;
+import jalview.analysis.*;
 import jalview.analysis.NJTree;
 import jalview.datamodel.*;
 import jalview.schemes.*;
@@ -15,19 +15,21 @@ public class AlignViewport
   int startSeq;
   int endSeq;
 
-  boolean showScores=false;
+  boolean showFullId = false;
   boolean showText=true;
   boolean showColourText=false;
   boolean showBoxes=true;
   boolean wrapAlignment=false;
-  boolean renderGaps = false;
-  boolean groupEdit    = false;
-  boolean groupDefiningMode = true;
+  boolean renderGaps = true;
+  boolean showSequenceFeatures = false;
+  boolean showAnnotation = true;
 
+  boolean colourAppliesToAllGroups = true;
   ColourSchemeI globalColourScheme = null;
   boolean conservationColourSelected = false;
+  boolean abovePIDThreshold = false;
 
-  SequenceGroup rubberbandGroup = null;
+  SequenceGroup selectionGroup = new SequenceGroup();
 
   RendererI renderer = new SequenceRenderer(this);
 
@@ -39,94 +41,153 @@ public class AlignViewport
   Font            font = new Font("SansSerif",Font.PLAIN,10);
   AlignmentI      alignment;
 
-  Selection       sel    = new Selection();
   ColumnSelection colSel = new ColumnSelection();
 
-  OutputGenerator og;
-
-  String visibleConsensus;
-
   int threshold;
   int increment;
 
   NJTree currentTree = null;
 
-  int window   = 50;
-  int baseline = 30;
 
-  Vector kmers;
-
-  public AlignViewport(AlignmentI da,
-                       boolean showScores,
+  public AlignViewport(AlignmentI al,
                        boolean showText,
                        boolean showBoxes,
                        boolean wrapAlignment) {
-    this(0,da.getWidth()-1,0,da.getHeight()-1,showScores,
-         showText,
-         showBoxes,
-         wrapAlignment);
 
-    setAlignment(da);
+    this.startRes = 0;
+    this.endRes = al.getWidth()-1;
+    this.startSeq = 0;
+    this.endSeq = al.getHeight()-1;
+    this.showText = showText;
+    this.showBoxes = showBoxes;
+    this.wrapAlignment = wrapAlignment;
+
+    setAlignment(al);
+    setFont( font );
+ }
+
+ public void showSequenceFeatures(boolean b)
+ {
+   showSequenceFeatures = b;
+ }
+
+  AlignmentAnnotation consensus;
+  AlignmentAnnotation conservation;
+  public void updateConservation()
+  {
+    Annotation [] annotations = new Annotation[alignment.getWidth()];
+
+    Conservation cons = new jalview.analysis.Conservation("All",
+        jalview.schemes.ResidueProperties.propHash, 3,
+        alignment.getSequences(), 0,
+        alignment.getWidth());
+    cons.calculate();
+    cons.verdict(false, 100);
+
+    String sequence = cons.getConsSequence().getSequence();
+    for (int i = 0; i < alignment.getWidth(); i++)
+    {
+      int value = 0;
+      try
+      {
+        value = Integer.parseInt(sequence.charAt(i) + "");
+      }
+      catch (Exception ex)
+      {
+        if (sequence.charAt(i) == '*') value = 10;
+      }
+
+      annotations[i] = new Annotation(sequence.charAt(i) + "",
+                                      "Conservation graph", ' ', value);
+    }
+
+    if(conservation==null)
+    {
+      conservation = new AlignmentAnnotation("Conservation",
+                                             "Conservation of total alignment",
+                                             annotations, 0, 10, 1);
+      alignment.addAnnotation(conservation);
+    }
+    else
+      conservation.annotations = annotations;
+
   }
 
-  public AlignViewport(int startRes, int endRes,
-                       int startSeq, int endSeq,
-                       boolean showScores,
-                       boolean showText,
-                       boolean showBoxes,
-                       boolean wrapAlignment) {
+  public void updateConsensus()
+  {
+    Annotation [] annotations = new Annotation[alignment.getWidth()];
 
-    this.startRes = startRes;
-    this.endRes   = endRes;
-    this.startSeq = startSeq;
-    this.endSeq   = endSeq;
+    Vector cons = alignment.getAAFrequency();
+    Hashtable hash = null;
+    for (int i = 0; i < alignment.getWidth(); i++)
+    {
+        hash = (Hashtable) cons.elementAt(i);
+        float value = Float.parseFloat(hash.get("maxCount").toString());
+        value /= Float.parseFloat(hash.get("size").toString());
+
+        value *= 100;
+        String maxRes = hash.get("maxResidue")+" ";
+        String mouseOver = hash.get("maxResidue")+" ";
+        if(maxRes.length()>2)
+        {
+          mouseOver = "["+maxRes+"] ";
+          maxRes = "+ ";
+        }
 
-    this.showScores    = showScores;
-    this.showText      = showText;
-    this.showBoxes     = showBoxes;
-    this.wrapAlignment = wrapAlignment;
+        mouseOver += (int)value+"%";
+        annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
 
-   // og  = new AlignmentOutputGenerator(this);
+    }
 
-    setFont( font );
- }
+     if(consensus==null)
+     {
+       consensus = new AlignmentAnnotation("% Identity",
+                                           "PID", annotations, 0f, 100f, 1);
+       alignment.addAnnotation(consensus);
+     }
+     else
+       consensus.annotations = annotations;
 
+  }
 
   public String getVisibleConsensus()
   {
     return visibleConsensus;
   }
 
-  Vector consensus = new Vector();
+  String visibleConsensus;
+  Vector consensusV = new Vector();
   public Vector getConsensus(boolean recalculate)
   {
-    if(recalculate || consensus.size()<1)
+    if(recalculate || consensusV.size()<1)
     {
-      consensus = alignment.getAAFrequency();
+      consensusV = alignment.getAAFrequency();
       StringBuffer sb = new StringBuffer();
       Hashtable hash = null;
-      for (int i = 0; i < consensus.size(); i++)
+      for (int i = 0; i < consensusV.size(); i++)
       {
-        hash = (Hashtable) consensus.elementAt(i);
+        hash = (Hashtable) consensusV.elementAt(i);
         sb.append(hash.get("maxResidue").toString().charAt(0));
       }
       visibleConsensus = sb.toString();
     }
 
 
-    return consensus;
+    return consensusV;
   }
 
-  public SequenceGroup getRubberbandGroup()
+
+  public SequenceGroup getSelectionGroup()
   {
-    return rubberbandGroup;
+    return selectionGroup;
   }
 
-  public void setRubberbandGroup(SequenceGroup sg)
+  public void setSelectionGroup(SequenceGroup sg)
   {
-    rubberbandGroup = sg;
+    selectionGroup = sg;
   }
 
+
  public boolean getConservationSelected()
  {
    return conservationColourSelected;
@@ -137,6 +198,16 @@ public class AlignViewport
    conservationColourSelected = b;
  }
 
+ public boolean getAbovePIDThreshold()
+ {
+   return abovePIDThreshold;
+ }
+
+ public void setAbovePIDThreshold(boolean b)
+ {
+   abovePIDThreshold = b;
+ }
+
   public int getStartRes() {
     return startRes;
   }
@@ -231,9 +302,7 @@ public class AlignViewport
   public void setAlignment(AlignmentI align) {
     this.alignment = align;
   }
-  public void setShowScores(boolean state) {
-    showScores = state;
-  }
+
   public void setWrapAlignment(boolean state) {
     wrapAlignment = state;
   }
@@ -264,9 +333,7 @@ public class AlignViewport
   public void setShowBoxes(boolean state) {
     showBoxes = state;
   }
-  public boolean getShowScores() {
-    return showScores;
-  }
+
   public boolean getWrapAlignment() {
       return wrapAlignment;
   }
@@ -276,15 +343,7 @@ public class AlignViewport
   public boolean getShowBoxes() {
     return showBoxes;
   }
- // public CommandParser getCommandLog() {
- ///   return log;
- // }
-  public boolean getGroupEdit() {
-    return groupEdit;
-  }
-  public void setGroupEdit(boolean state) {
-    groupEdit = state;
-  }
+
   public char getGapCharacter() {
     return getAlignment().getGapCharacter();
   }
@@ -324,17 +383,12 @@ public class AlignViewport
     }
     return -1;
   }
-  public Selection getSelection() {
-    return sel;
-  }
+
   public ColumnSelection getColumnSelection() {
     return colSel;
   }
-  public OutputGenerator getOutputGenerator() {
-    return og;
-  }
+
   public void resetSeqLimits(int height) {
-    setStartSeq(0);
     setEndSeq(height/getCharHeight());
   }
   public void setCurrentTree(NJTree tree) {
@@ -351,27 +405,31 @@ public class AlignViewport
     public RendererI getRenderer() {
 	return renderer;
     }
-    public int getPIDWindow() {
-	return window;
-    }
-    public void setPIDWindow(int window) {
-	this.window = window;
-    }
 
-    public int getPIDBaseline() {
-	return baseline;
-    }
-    public void setPIDBaseline(int baseline) {
-	this.baseline = baseline;
-    }
+  public void setColourAppliesToAllGroups(boolean b)
+  {   colourAppliesToAllGroups = b; }
 
-    public void setKmers(Vector kmers) {
-        this.kmers = kmers;
-    }
+  public boolean getColourAppliesToAllGroups()
+  {return colourAppliesToAllGroups; }
 
-    public Vector getKmers() {
-        return this.kmers;
-    }
+  public boolean getShowFullId()
+  {
+    return showFullId;
+  }
 
+  public void setShowFullId(boolean b)
+  {
+    showFullId = b;
+  }
+
+  public boolean getShowAnnotation()
+  {
+    return showAnnotation;
+  }
+
+  public void setShowAnnotation(boolean b)
+  {
+    showAnnotation = b;
+  }
 
 }