X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=5535dbbaf3bbb5690e0dba43835e47134b7ebcfa;hb=90925a374cc14797c3e353f30af938a2eec025a8;hp=7719f024b8ed750bea0db1900adc0a288e46b416;hpb=f4e3be3ba13e6a575140983b46ac84e919184eee;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7719f02..5535dbb 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.*;
@@ -15,20 +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 = 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);
 
@@ -40,49 +41,32 @@ public class AlignViewport
   Font            font = new Font("SansSerif",Font.PLAIN,10);
   AlignmentI      alignment;
 
-  Selection       sel    = new Selection(this);
   ColumnSelection colSel = new ColumnSelection();
 
-  String visibleConsensus;
-
   int threshold;
   int increment;
 
   NJTree currentTree = null;
 
+  boolean scaleAboveWrapped = false;
+  boolean scaleLeftWrapped  = true;
+  boolean scaleRightWrapped = true;
 
-  public AlignViewport(AlignmentI da,
-                       boolean showScores,
-                       boolean showText,
-                       boolean showBoxes,
-                       boolean wrapAlignment) {
-    this(0,da.getWidth()-1,0,da.getHeight()-1,showScores,
-         showText,
-         showBoxes,
-         wrapAlignment);
-
-    setAlignment(da);
-  }
 
-  public AlignViewport(int startRes, int endRes,
-                       int startSeq, int endSeq,
-                       boolean showScores,
+  public AlignViewport(AlignmentI al,
                        boolean showText,
                        boolean showBoxes,
                        boolean wrapAlignment) {
 
-    this.startRes = startRes;
-    this.endRes   = endRes;
-    this.startSeq = startSeq;
-    this.endSeq   = endSeq;
-
-    this.showScores    = showScores;
-    this.showText      = showText;
-    this.showBoxes     = showBoxes;
+    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;
 
-   // og  = new AlignmentOutputGenerator(this);
-
+    setAlignment(al);
     setFont( font );
  }
 
@@ -91,41 +75,158 @@ public class AlignViewport
    showSequenceFeatures = b;
  }
 
+  AlignmentAnnotation consensus;
+  AlignmentAnnotation conservation;
+  AlignmentAnnotation quality;
+
+  public void updateConservation()
+  {
+    int percGaps = 100; // JBPNote : This should be a scalable property!
+    Conservation cons = new jalview.analysis.Conservation("All",
+        jalview.schemes.ResidueProperties.propHash, 1,
+        alignment.getSequences(), 0,
+        alignment.getWidth());
+    cons.calculate();
+    cons.verdict(false, percGaps);
+    cons.findQuality();
+    int alWidth = alignment.getWidth();
+    Annotation [] annotations = new Annotation[alWidth];
+    Annotation [] qannotations = new Annotation[alWidth];
+    String sequence = cons.getConsSequence().getSequence();
+    float minR,minG,minB, maxR,maxG,maxB;
+    minR = 0.3f;
+    minG = 0.0f;
+    minB = 0f;
+    maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring both Conservation and Quality
+    float min = 0f;
+    float max = 11f;
+    float qmin = cons.qualityRange[0].floatValue();
+    float qmax = cons.qualityRange[1].floatValue();
+
+    for (int i = 0; i < alWidth; i++)
+    {
+      float value = 0;
+      try
+        {
+          value = Integer.parseInt(sequence.charAt(i) + "");
+        }
+      catch (Exception ex)
+        {
+          if (sequence.charAt(i) == '*') value = 11;
+          if (sequence.charAt(i) == '+') value = 10;
+        }
+      float vprop = value-min;
+      vprop/=max;
+      annotations[i] = new Annotation(sequence.charAt(i) + "",
+                                      "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
+      // Quality calc
+      value = ((Double) cons.quality.get(i)).floatValue();
+      vprop = value - qmin;
+      vprop/=qmax;
+      qannotations[i] = new Annotation(sequence.charAt(i) + "",
+                                      new String().valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
+    }
+
+    if(conservation==null)
+    {
+      conservation = new AlignmentAnnotation("Conservation",
+                                             "Conservation of total alignment less than "+percGaps+"% gaps",
+                                             annotations,
+                                             0f, // cons.qualityRange[0].floatValue(),
+                                             11f, // cons.qualityRange[1].floatValue()
+                                             1);
+      alignment.addAnnotation(conservation);
+      quality = new AlignmentAnnotation("Quality",
+                                        "Alignment Quality based on Blosum62 scores",
+                                        qannotations,
+                                        cons.qualityRange[0].floatValue(),
+                                        cons.qualityRange[1].floatValue(),
+                                        1);
+      alignment.addAnnotation(quality);
+    }
+    else {
+      conservation.annotations = annotations;
+      quality.annotations = qannotations;
+    }
+
+
+  }
+
+  public void updateConsensus()
+  {
+    Annotation [] annotations = new Annotation[alignment.getWidth()];
+
+    Vector cons = alignment.getAAFrequency();
+    Hashtable hash = null;
+    for (int i = 0, alWidth=alignment.getWidth(); i<alWidth; 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 = "+ ";
+        }
+
+        mouseOver += (int)value+"%";
+        annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+
+    }
+
+     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, sz=consensusV.size(); i < sz; 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;
@@ -178,7 +279,7 @@ public class AlignViewport
   public void setEndRes(int res) {
     if (res > alignment.getWidth()-1) {
       System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-       res = alignment.getWidth() -1;
+       res = alignment.getWidth()-1;
     }
     if (res < 0) {
       res = 0;
@@ -240,9 +341,7 @@ 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;
   }
@@ -273,9 +372,7 @@ public class AlignViewport
   public void setShowBoxes(boolean state) {
     showBoxes = state;
   }
-  public boolean getShowScores() {
-    return showScores;
-  }
+
   public boolean getWrapAlignment() {
       return wrapAlignment;
   }
@@ -325,15 +422,12 @@ public class AlignViewport
     }
     return -1;
   }
-  public Selection getSelection() {
-    return sel;
-  }
+
   public ColumnSelection getColumnSelection() {
     return colSel;
   }
 
   public void resetSeqLimits(int height) {
-    setStartSeq(0);
     setEndSeq(height/getCharHeight());
   }
   public void setCurrentTree(NJTree tree) {
@@ -357,5 +451,43 @@ public class AlignViewport
   public boolean getColourAppliesToAllGroups()
   {return colourAppliesToAllGroups; }
 
+  public boolean getShowFullId()
+  {
+    return showFullId;
+  }
+
+  public void setShowFullId(boolean b)
+  {
+    showFullId = b;
+  }
+
+  public boolean getShowAnnotation()
+  {
+    return showAnnotation;
+  }
+
+  public void setShowAnnotation(boolean b)
+  {
+    showAnnotation = b;
+  }
+
+  public boolean getScaleAboveWrapped()
+  { return scaleAboveWrapped;}
+
+  public boolean getScaleLeftWrapped()
+  { return scaleLeftWrapped; }
+
+  public boolean getScaleRightWrapped()
+  { return scaleRightWrapped; }
+
+  public void setScaleAboveWrapped(boolean b)
+  { scaleAboveWrapped = b; }
+
+  public void setScaleLeftWrapped(boolean b)
+  { scaleLeftWrapped = b; }
+
+  public void setScaleRightWrapped(boolean b)
+  { scaleRightWrapped = b; }
+
 
 }