X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=51478f22f04a367394e66acf9f4c36762d364b72;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=cef87f7ca9b76497471470ebd6fca82a902742c9;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index cef87f7..51478f2 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,11 +1,32 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
 package jalview.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
-import jalview.bin.*;
+
 import jalview.analysis.*;
+import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.util.*;
 
 public class AlignViewport
 {
@@ -16,10 +37,10 @@ public class AlignViewport
   int endSeq;
 
   boolean showFullId = true;
-  boolean showText=true;
-  boolean showColourText=false;
-  boolean showBoxes=true;
-  boolean wrapAlignment=false;
+  boolean showText = true;
+  boolean showColourText = false;
+  boolean showBoxes = true;
+  boolean wrapAlignment = false;
   boolean renderGaps = true;
   boolean showSequenceFeatures = false;
   boolean showAnnotation = true;
@@ -34,13 +55,13 @@ public class AlignViewport
 
   SequenceGroup selectionGroup = new SequenceGroup();
 
-  int             charHeight;
-  int             charWidth;
-  int             chunkWidth;
-  int             chunkHeight;
+  int charHeight;
+  int charWidth;
+  int chunkWidth;
+  int chunkHeight;
 
-  Font            font = new Font("SansSerif",Font.PLAIN,10);
-  AlignmentI      alignment;
+  Font font = new Font("SansSerif", Font.PLAIN, 10);
+  AlignmentI alignment;
 
   ColumnSelection colSel = new ColumnSelection();
 
@@ -50,60 +71,70 @@ public class AlignViewport
   NJTree currentTree = null;
 
   boolean scaleAboveWrapped = true;
-  boolean scaleLeftWrapped  = true;
+  boolean scaleLeftWrapped = true;
   boolean scaleRightWrapped = true;
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     setAlignment(al);
     this.startRes = 0;
-    this.endRes = al.getWidth()-1;
+    this.endRes = al.getWidth() - 1;
     this.startSeq = 0;
-    this.endSeq = al.getHeight()-1;
+    this.endSeq = al.getHeight() - 1;
     setFont(font);
 
-
-    if(applet!=null)
+    if (applet != null)
     {
       String param = applet.getParameter("showFullId");
       if (param != null)
+      {
         showFullId = Boolean.valueOf(param).booleanValue();
+      }
 
       param = applet.getParameter("showAnnotation");
       if (param != null)
+      {
         showAnnotation = Boolean.valueOf(param).booleanValue();
+      }
 
       param = applet.getParameter("showConservation");
       if (param != null)
+      {
         showConservation = Boolean.valueOf(param).booleanValue();
+      }
 
       param = applet.getParameter("showQuality");
       if (param != null)
+      {
         showQuality = Boolean.valueOf(param).booleanValue();
+      }
 
       param = applet.getParameter("showConsensus");
       if (param != null)
+      {
         showConsensus = Boolean.valueOf(param).booleanValue();
+      }
     }
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
     updateConservation();
     updateConsensus();
 
-    if(applet!=null && applet.getParameter("defaultColour")!=null)
+    if (applet != null && applet.getParameter("defaultColour") != null)
     {
       globalColourScheme = ColourSchemeProperty.getColour(alignment,
           applet.getParameter("defaultColour"));
-      if(globalColourScheme!=null)
-        globalColourScheme.setConsensus( vconsensus );
-   }
- }
-
+      if (globalColourScheme != null)
+      {
+        globalColourScheme.setConsensus(vconsensus);
+      }
+    }
+  }
 
- public void showSequenceFeatures(boolean b)
- {
-   showSequenceFeatures = b;
- }
+  public void showSequenceFeatures(boolean b)
+  {
+    showSequenceFeatures = b;
+  }
 
   public Vector vconsensus;
   AlignmentAnnotation consensus;
@@ -117,19 +148,21 @@ public class AlignViewport
     Conservation cons = new jalview.analysis.Conservation("All",
         jalview.schemes.ResidueProperties.propHash, 3,
         alignment.getSequences(), 0,
-        alignment.getWidth()-1);
+        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];
+    Annotation[] annotations = new Annotation[alWidth];
+    Annotation[] qannotations = new Annotation[alWidth];
     String sequence = cons.getConsSequence().getSequence();
-    float minR,minG,minB, maxR,maxG,maxB;
+    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
+    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();
@@ -139,107 +172,131 @@ public class AlignViewport
     {
       float value = 0;
       try
+      {
+        value = Integer.parseInt(sequence.charAt(i) + "");
+      }
+      catch (Exception ex)
+      {
+        if (sequence.charAt(i) == '*')
         {
-          value = Integer.parseInt(sequence.charAt(i) + "");
+          value = 11;
         }
-      catch (Exception ex)
+        if (sequence.charAt(i) == '+')
         {
-          if (sequence.charAt(i) == '*') value = 11;
-          if (sequence.charAt(i) == '+') value = 10;
+          value = 10;
         }
-      float vprop = value-min;
-      vprop/=max;
+      }
+      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));
+                                      "", ' ', value,
+                                      new Color(minR + maxR * vprop,
+                                                minG + maxG * vprop,
+                                                minB + maxB * vprop));
       // Quality calc
-      value = ((Double) cons.quality.elementAt(i)).floatValue();
+      value = ( (Double) cons.quality.elementAt(i)).floatValue();
       vprop = value - qmin;
-      vprop/=qmax;
+      vprop /= qmax;
       qannotations[i] = new Annotation(" ",
-                                      String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
+                                       String.valueOf(value), ' ', value,
+                                       new
+                                       Color(minR + maxR * vprop,
+                                             minG + maxG * vprop,
+                                             minB + maxB * vprop));
     }
 
-    if(conservation==null)
+    if (conservation == null)
     {
       conservation = new AlignmentAnnotation("Conservation",
-                                             "Conservation of total alignment less than "+ConsPercGaps+"% gaps",
+                                             "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);
+      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)
+      if (showQuality)
+      {
         alignment.addAnnotation(quality);
+      }
     }
-    else {
+    else
+    {
       conservation.annotations = annotations;
       quality.annotations = qannotations;
       quality.graphMax = cons.qualityRange[1].floatValue();
     }
 
-
   }
 
   public void updateConsensus()
   {
-    Annotation [] annotations = new Annotation[alignment.getWidth()];
+    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();
+    if (vconsensus == null)
+    {
+      vconsensus = alignment.getAAFrequency();
+    }
     else
     {
-        Vector temp = alignment.getAAFrequency();
-        vconsensus.removeAllElements();
-        Enumeration e = temp.elements();
-        while(e.hasMoreElements())
-        {
-          vconsensus.addElement(e.nextElement());
-        }
+      Vector temp = alignment.getAAFrequency();
+      vconsensus.removeAllElements();
+      Enumeration e = temp.elements();
+      while (e.hasMoreElements())
+      {
+        vconsensus.addElement(e.nextElement());
+      }
     }
     Hashtable hash = null;
-    for (int i = 0; i<alignment.getWidth(); i++)
+    for (int i = 0; i < alignment.getWidth(); i++)
     {
-        hash = (Hashtable) vconsensus.elementAt(i);
-        float value = new Float(hash.get("maxCount").toString()).floatValue();
-        value /= new Float(hash.get("size").toString()).floatValue();
-
-        value *= 100;
-        String maxRes = hash.get("maxResidue")+" ";
-        String mouseOver = hash.get("maxResidue")+" ";
-        if(maxRes.length()>2)
-        {
-          mouseOver = "["+maxRes+"] ";
-          maxRes = "+ ";
-        }
+      hash = (Hashtable) vconsensus.elementAt(i);
+      float value = new Float(hash.get("maxCount").toString()).floatValue();
+      value /= new Float(hash.get("size").toString()).floatValue();
+
+      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);
+      mouseOver += (int) value + "%";
+      annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
 
     }
 
-     if(consensus==null)
-     {
-       consensus = new AlignmentAnnotation("Consensus",
-                                           "PID", annotations, 0f, 100f, 1);
-       if(showConsensus)
-         alignment.addAnnotation(consensus);
-     }
-     else
-       consensus.annotations = annotations;
+    if (consensus == null)
+    {
+      consensus = new AlignmentAnnotation("Consensus",
+                                          "PID", annotations, 0f, 100f, 1);
+      if (showConsensus)
+      {
+        alignment.addAnnotation(consensus);
+      }
+    }
+    else
+    {
+      consensus.annotations = annotations;
+    }
 
   }
 
-
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -250,42 +307,44 @@ public class AlignViewport
     selectionGroup = sg;
   }
 
+  public boolean getConservationSelected()
+  {
+    return conservationColourSelected;
+  }
 
- public boolean getConservationSelected()
- {
-   return conservationColourSelected;
- }
-
- public void setConservationSelected(boolean b)
- {
-   conservationColourSelected = b;
- }
+  public void setConservationSelected(boolean b)
+  {
+    conservationColourSelected = b;
+  }
 
- public boolean getAbovePIDThreshold()
- {
-   return abovePIDThreshold;
- }
+  public boolean getAbovePIDThreshold()
+  {
+    return abovePIDThreshold;
+  }
 
- public void setAbovePIDThreshold(boolean b)
- {
-   abovePIDThreshold = b;
- }
+  public void setAbovePIDThreshold(boolean b)
+  {
+    abovePIDThreshold = b;
+  }
 
-  public int getStartRes() {
+  public int getStartRes()
+  {
     return startRes;
   }
 
-  public int getEndRes() {
+  public int getEndRes()
+  {
     return endRes;
   }
 
-  public int getStartSeq() {
+  public int getStartSeq()
+  {
     return startSeq;
   }
 
   public void setGlobalColourScheme(ColourSchemeI cs)
   {
-     globalColourScheme = cs;
+    globalColourScheme = cs;
   }
 
   public ColourSchemeI getGlobalColourScheme()
@@ -293,37 +352,50 @@ public class AlignViewport
     return globalColourScheme;
   }
 
-
-  public void setStartRes(int res) {
+  public void setStartRes(int res)
+  {
     this.startRes = res;
   }
-  public void setStartSeq(int seq) {
+
+  public void setStartSeq(int seq)
+  {
     this.startSeq = seq;
   }
-  public void setEndRes(int res) {
-    if (res > alignment.getWidth()-1) {
+
+  public void setEndRes(int res)
+  {
+    if (res > alignment.getWidth() - 1)
+    {
       // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-       res = alignment.getWidth()-1;
+      res = alignment.getWidth() - 1;
     }
-    if (res < 0) {
+    if (res < 0)
+    {
       res = 0;
     }
     this.endRes = res;
   }
-  public void setEndSeq(int seq) {
-    if (seq > alignment.getHeight()) {
+
+  public void setEndSeq(int seq)
+  {
+    if (seq > alignment.getHeight())
+    {
       seq = alignment.getHeight();
     }
-    if (seq < 0) {
+    if (seq < 0)
+    {
       seq = 0;
     }
     this.endSeq = seq;
   }
-  public int getEndSeq() {
+
+  public int getEndSeq()
+  {
     return endSeq;
   }
 
-  public void setFont(Font f) {
+  public void setFont(Font f)
+  {
     font = f;
     java.awt.Frame temp = new java.awt.Frame();
     temp.addNotify();
@@ -332,52 +404,76 @@ public class AlignViewport
     setCharWidth(fm.charWidth('M'));
   }
 
-  public Font getFont() {
+  public Font getFont()
+  {
     return font;
   }
-  public void setCharWidth(int w) {
+
+  public void setCharWidth(int w)
+  {
     this.charWidth = w;
   }
-  public int getCharWidth() {
+
+  public int getCharWidth()
+  {
     return charWidth;
   }
-  public void setCharHeight(int h) {
+
+  public void setCharHeight(int h)
+  {
     this.charHeight = h;
   }
-  public int getCharHeight() {
+
+  public int getCharHeight()
+  {
     return charHeight;
   }
-  public void setChunkWidth(int w) {
+
+  public void setChunkWidth(int w)
+  {
     this.chunkWidth = w;
   }
-  public int getChunkWidth() {
+
+  public int getChunkWidth()
+  {
     return chunkWidth;
   }
-  public void setChunkHeight(int h) {
+
+  public void setChunkHeight(int h)
+  {
     this.chunkHeight = h;
   }
-  public int getChunkHeight() {
+
+  public int getChunkHeight()
+  {
     return chunkHeight;
   }
-  public AlignmentI getAlignment() {
+
+  public AlignmentI getAlignment()
+  {
     return alignment;
   }
-  public void setAlignment(AlignmentI align) {
+
+  public void setAlignment(AlignmentI align)
+  {
     this.alignment = align;
   }
 
-  public void setWrapAlignment(boolean state) {
+  public void setWrapAlignment(boolean state)
+  {
     wrapAlignment = state;
   }
-  public void setShowText(boolean state) {
+
+  public void setShowText(boolean state)
+  {
     showText = state;
   }
 
-  public void setRenderGaps(boolean state){
+  public void setRenderGaps(boolean state)
+  {
     renderGaps = state;
   }
 
-
   public boolean getColourText()
   {
     return showColourText;
@@ -388,80 +484,114 @@ public class AlignViewport
     showColourText = state;
   }
 
-  public void setShowBoxes(boolean state) {
+  public void setShowBoxes(boolean state)
+  {
     showBoxes = state;
   }
 
-  public boolean getWrapAlignment() {
-      return wrapAlignment;
+  public boolean getWrapAlignment()
+  {
+    return wrapAlignment;
   }
-  public boolean getShowText() {
+
+  public boolean getShowText()
+  {
     return showText;
   }
-  public boolean getShowBoxes() {
+
+  public boolean getShowBoxes()
+  {
     return showBoxes;
   }
 
-  public char getGapCharacter() {
+  public char getGapCharacter()
+  {
     return getAlignment().getGapCharacter();
   }
-  public void setGapCharacter(char gap) {
-    if (getAlignment() != null) {
+
+  public void setGapCharacter(char gap)
+  {
+    if (getAlignment() != null)
+    {
       getAlignment().setGapCharacter(gap);
     }
   }
-  public void setThreshold(int thresh) {
+
+  public void setThreshold(int thresh)
+  {
     threshold = thresh;
   }
-  public int getThreshold() {
+
+  public int getThreshold()
+  {
     return threshold;
   }
-  public void setIncrement(int inc) {
+
+  public void setIncrement(int inc)
+  {
     increment = inc;
   }
-  public int getIncrement() {
+
+  public int getIncrement()
+  {
     return increment;
   }
-  public int getIndex(int y) {
-    int y1     = 0;
+
+  public int getIndex(int y)
+  {
+    int y1 = 0;
     int starty = getStartSeq();
-    int endy   = getEndSeq();
+    int endy = getEndSeq();
 
-    for (int i = starty; i <= endy; i++) {
-      if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {
+    for (int i = starty; i <= endy; i++)
+    {
+      if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null)
+      {
         int y2 = y1 + getCharHeight();
 
-        if (y>=y1 && y <=y2) {
+        if (y >= y1 && y <= y2)
+        {
           return i;
         }
-        y1  = y2;
-      } else {
+        y1 = y2;
+      }
+      else
+      {
         return -1;
       }
     }
     return -1;
   }
 
-  public ColumnSelection getColumnSelection() {
+  public ColumnSelection getColumnSelection()
+  {
     return colSel;
   }
 
-  public void resetSeqLimits(int height) {
-    setEndSeq(height/getCharHeight());
+  public void resetSeqLimits(int height)
+  {
+    setEndSeq(height / getCharHeight());
   }
-  public void setCurrentTree(NJTree tree) {
-      currentTree = tree;
+
+  public void setCurrentTree(NJTree tree)
+  {
+    currentTree = tree;
   }
-  public NJTree getCurrentTree() {
+
+  public NJTree getCurrentTree()
+  {
     return currentTree;
   }
 
-
   public void setColourAppliesToAllGroups(boolean b)
-  {   colourAppliesToAllGroups = b; }
+  {
+    colourAppliesToAllGroups = b;
+  }
 
   public boolean getColourAppliesToAllGroups()
-  {return colourAppliesToAllGroups; }
+  {
+    return colourAppliesToAllGroups;
+  }
 
   public boolean getShowFullId()
   {
@@ -484,22 +614,33 @@ public class AlignViewport
   }
 
   public boolean getScaleAboveWrapped()
-  { return scaleAboveWrapped;}
+  {
+    return scaleAboveWrapped;
+  }
 
   public boolean getScaleLeftWrapped()
-  { return scaleLeftWrapped; }
+  {
+    return scaleLeftWrapped;
+  }
 
   public boolean getScaleRightWrapped()
-  { return scaleRightWrapped; }
+  {
+    return scaleRightWrapped;
+  }
 
   public void setScaleAboveWrapped(boolean b)
-  { scaleAboveWrapped = b; }
+  {
+    scaleAboveWrapped = b;
+  }
 
   public void setScaleLeftWrapped(boolean b)
-  { scaleLeftWrapped = b; }
+  {
+    scaleLeftWrapped = b;
+  }
 
   public void setScaleRightWrapped(boolean b)
-  { scaleRightWrapped = b; }
-
+  {
+    scaleRightWrapped = b;
+  }
 
 }