X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=98fd229af7d9233f1348bb5b68776d1a2a5e3ee0;hb=85867b5d46751cfce6500002e098a431fec0950e;hp=905255a11536bf27745f262fc94d1b4d7c3185a5;hpb=157004a864888ed2e690b907a28f715d3d42b666;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 905255a..98fd229 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,11 +1,12 @@
 package jalview.gui;
 
 import java.awt.*;
-import jalview.io.*;
+import jalview.analysis.*;
 import jalview.analysis.NJTree;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 import java.util.*;
+import jalview.bin.Cache;
 
 public class AlignViewport
 {
@@ -15,106 +16,268 @@ 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 showConservation = true;
+  boolean showQuality = true;
+  boolean showIdentity = true;
+
+  boolean colourAppliesToAllGroups = true;
   ColourSchemeI globalColourScheme = null;
+  boolean conservationColourSelected = false;
+  boolean abovePIDThreshold = false;
+
+  SequenceGroup selectionGroup = new SequenceGroup();
 
   RendererI renderer = new SequenceRenderer(this);
 
   int             charHeight;
-  int          charWidth;
+  int             charWidth;
   int             chunkWidth;
   int             chunkHeight;
 
   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;
+  boolean scaleAboveWrapped = false;
+  boolean scaleLeftWrapped  = true;
+  boolean scaleRightWrapped = true;
+
 
-  Vector kmers;
+  public AlignViewport(AlignmentI al)
+  {
+    setAlignment(al);
+    this.startRes = 0;
+    this.endRes = al.getWidth()-1;
+    this.startSeq = 0;
+    this.endSeq = al.getHeight()-1;
 
-  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);
+    updateFromPreferences();
 
-    setAlignment(da);
   }
 
-  public AlignViewport(int startRes, int endRes,
-                       int startSeq, int endSeq,
-                       boolean showScores,
-                       boolean showText,
-                       boolean showBoxes,
-                       boolean wrapAlignment) {
+  public void updateFromPreferences()
+  {
+    showFullId = Preferences.showFullId;
+    showAnnotation = Preferences.showAnnotation;
+    showConservation = Preferences.showConservation;
+    showQuality = Preferences.showQuality;
+    showIdentity = Preferences.showIdentity;
+    showFullId = Preferences.showFullId;
+    String fontName = Preferences.fontName;
+    String fontStyle = Preferences.fontStyle;
+    String fontSize = Cache.getProperty("FONT_SIZE");
+    if (fontName != null && fontStyle != null && fontSize != null)
+    {
+      int style = 0;
+      if(fontStyle.equals("bold"))
+        style = 1;
+      else if(fontStyle.equals("italic"))
+        style = 2;
+      setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+    }
+    else
+      setFont(font);
 
-    this.startRes = startRes;
-    this.endRes   = endRes;
-    this.startSeq = startSeq;
-    this.endSeq   = endSeq;
+    alignment.setGapCharacter(Preferences.gapSymbol);
 
-    this.showScores    = showScores;
-    this.showText      = showText;
-    this.showBoxes     = showBoxes;
-    this.wrapAlignment = wrapAlignment;
+    // We must set conservation and consensus before setting colour,
+    // as Blosum and Clustal require this to be done
+    updateConservation();
+    updateConsensus();
+    if(Preferences.defaultColour!=null)
+    {
+      globalColourScheme = ColourSchemeProperty.getColour(alignment, Preferences.defaultColour);
+      if(globalColourScheme!=null)
+        globalColourScheme.setConsensus( vconsensus );
+   }
 
-   // og  = new AlignmentOutputGenerator(this);
+ }
 
-    setFont( font );
+ public void showSequenceFeatures(boolean b)
+ {
+   showSequenceFeatures = b;
  }
 
+  public Vector vconsensus;
+  AlignmentAnnotation consensus;
+  AlignmentAnnotation conservation;
+  AlignmentAnnotation quality;
+
+  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
-  public String getVisibleConsensus()
+  public void updateConservation()
   {
-    return visibleConsensus;
+    Conservation cons = new jalview.analysis.Conservation("All",
+        jalview.schemes.ResidueProperties.propHash, 3,
+        alignment.getSequences(), 0,
+        alignment.getWidth()-1);
+    cons.calculate();
+    cons.verdict(false, ConsPercGaps);
+    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(" ",
+                                      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 "+ConsPercGaps+"% gaps",
+                                             annotations,
+                                             0f, // cons.qualityRange[0].floatValue(),
+                                             11f, // cons.qualityRange[1].floatValue()
+                                             1);
+      if(showConservation)
+      alignment.addAnnotation(conservation);
+      quality = new AlignmentAnnotation("Quality",
+                                        "Alignment Quality based on Blosum62 scores",
+                                        qannotations,
+                                        cons.qualityRange[0].floatValue(),
+                                        cons.qualityRange[1].floatValue(),
+                                        1);
+      if(showQuality)
+        alignment.addAnnotation(quality);
+    }
+    else {
+      conservation.annotations = annotations;
+      quality.annotations = qannotations;
+      quality.graphMax = cons.qualityRange[1].floatValue();
+    }
+
+
   }
 
-  Vector consensus = new Vector();
-  public Vector getConsensus(boolean recalculate)
+  public void updateConsensus()
   {
-    if(recalculate || consensus.size()<1)
+    Annotation [] annotations = new Annotation[alignment.getWidth()];
+
+    // this routine prevents vconsensus becoming a new object each time
+    // consenus is calculated. Important for speed of Blosum62
+    // and PID colouring of alignment
+    if(vconsensus == null)
+        vconsensus = alignment.getAAFrequency();
+    else
     {
-      consensus = alignment.getAAFrequency();
-      StringBuffer sb = new StringBuffer();
-      Hashtable hash = null;
-      for (int i = 0; i < consensus.size(); i++)
-      {
-        hash = (Hashtable) consensus.elementAt(i);
-        sb.append(hash.get("maxResidue").toString().charAt(0));
-      }
-      visibleConsensus = sb.toString();
+        Vector temp = alignment.getAAFrequency();
+        vconsensus.clear();
+        Enumeration e = temp.elements();
+        while(e.hasMoreElements())
+        {
+          vconsensus.add(e.nextElement());
+        }
+    }
+    Hashtable hash = null;
+    for (int i = 0; i<alignment.getWidth(); i++)
+    {
+        hash = (Hashtable) vconsensus.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);
+       if(showIdentity)
+         alignment.addAnnotation(consensus);
+     }
+     else
+       consensus.annotations = annotations;
 
-    return consensus;
   }
 
 
+  public SequenceGroup getSelectionGroup()
+  {
+    return selectionGroup;
+  }
+
+  public void setSelectionGroup(SequenceGroup sg)
+  {
+    selectionGroup = sg;
+  }
+
+
+ public boolean getConservationSelected()
+ {
+   return conservationColourSelected;
+ }
+
+ public void setConservationSelected(boolean b)
+ {
+   conservationColourSelected = b;
+ }
+
+ public boolean getAbovePIDThreshold()
+ {
+   return abovePIDThreshold;
+ }
+
+ public void setAbovePIDThreshold(boolean b)
+ {
+   abovePIDThreshold = b;
+ }
+
   public int getStartRes() {
     return startRes;
   }
@@ -147,7 +310,7 @@ 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;
@@ -209,9 +372,7 @@ 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;
   }
@@ -242,9 +403,7 @@ public class AlignViewport
   public void setShowBoxes(boolean state) {
     showBoxes = state;
   }
-  public boolean getShowScores() {
-    return showScores;
-  }
+
   public boolean getWrapAlignment() {
       return wrapAlignment;
   }
@@ -254,15 +413,7 @@ 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();
   }
@@ -302,17 +453,12 @@ 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) {
@@ -329,27 +475,50 @@ 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;
+  }
+
+  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; }
 
 
 }