X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=729096bd70f9ff7d53f6a3e4f4375960185390c0;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=cc04b581000251b40d94935b01f29c997dcdd1a7;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index cc04b58..729096b 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,103 +1,61 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
+import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.bin.JalviewLite;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.CommandListener;
 import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.Font;
+
 public class AlignViewport extends AlignmentViewport implements
-        AlignViewportI, SelectionSource, VamsasSource
+        SelectionSource, VamsasSource, CommandListener
 {
-  int startRes;
-
-  int endRes;
-
-  int startSeq;
-
-  int endSeq;
-
   boolean cursorMode = false;
 
-  boolean showJVSuffix = true;
-
-  boolean showText = true;
-
-  boolean showColourText = false;
-
-  boolean showBoxes = true;
-
-  boolean wrapAlignment = false;
-
-  boolean renderGaps = true;
-
-  boolean showSequenceFeatures = false;
-
-  boolean showAnnotation = true;
-
-  boolean upperCasebold = false;
-
-  int charHeight;
-
-  int charWidth;
-
-  int wrappedWidth;
-
   Font font = new Font("SansSerif", Font.PLAIN, 10);
 
   boolean validCharWidth = true;
 
-  int threshold;
-
-  int increment;
-
   NJTree currentTree = null;
 
-  boolean scaleAboveWrapped = true;
-
-  boolean scaleLeftWrapped = true;
-
-  boolean scaleRightWrapped = true;
-
-  // The following vector holds the features which are
-  // currently visible, in the correct order or rendering
-  public Hashtable featuresDisplayed;
-
-  boolean showHiddenMarkers = true;
-
   public jalview.bin.JalviewLite applet;
 
-  Hashtable sequenceColours;
-
   boolean MAC = false;
 
-  Stack historyList = new Stack();
-
-  Stack redoList = new Stack();
+  private AnnotationColumnChooser annotationColumnSelectionState;
 
   public void finalize()
   {
@@ -109,9 +67,10 @@ public class AlignViewport extends AlignmentViewport implements
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
+    super();
     calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
-    setAlignment(al);
+    alignment = al;
     // we always pad gaps
     this.setPadGaps(true);
     this.startRes = 0;
@@ -137,7 +96,7 @@ public class AlignViewport extends AlignmentViewport implements
                           + widthScale + "). Ignoring.");
           widthScale = 1;
         }
-        if (applet.debug)
+        if (JalviewLite.debug)
         {
           System.err
                   .println("Alignment character width scaling factor is now "
@@ -160,7 +119,7 @@ public class AlignViewport extends AlignmentViewport implements
                           + heightScale + "). Ignoring.");
           heightScale = 1;
         }
-        if (applet.debug)
+        if (JalviewLite.debug)
         {
           System.err
                   .println("Alignment character height scaling factor is now "
@@ -174,10 +133,11 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (applet != null)
     {
-      showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
+      setShowJVSuffix(applet.getDefaultParameter("showFullId",
+              getShowJVSuffix()));
 
-      showAnnotation = applet.getDefaultParameter("showAnnotation",
-              showAnnotation);
+      setShowAnnotation(applet.getDefaultParameter("showAnnotation",
+              isShowAnnotation()));
 
       showConservation = applet.getDefaultParameter("showConservation",
               showConservation);
@@ -187,22 +147,25 @@ public class AlignViewport extends AlignmentViewport implements
       showConsensus = applet.getDefaultParameter("showConsensus",
               showConsensus);
 
-      showUnconserved = applet.getDefaultParameter("showUnconserved",
-              showUnconserved);
+      setShowUnconserved(applet.getDefaultParameter("showUnconserved",
+              getShowUnconserved()));
+
+      setScaleProteinAsCdna(applet.getDefaultParameter(
+              "scaleProteinAsCdna", isScaleProteinAsCdna()));
 
       String param = applet.getParameter("upperCase");
       if (param != null)
       {
         if (param.equalsIgnoreCase("bold"))
         {
-          upperCasebold = true;
+          setUpperCasebold(true);
         }
       }
       sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
 
-      followHighlight = applet.getDefaultParameter("automaticScrolling",
-              followHighlight);
-      followSelection = followHighlight;
+      setFollowHighlight(applet.getDefaultParameter("automaticScrolling",
+              isFollowHighlight()));
+      followSelection = isFollowHighlight();
 
       showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
               showSequenceLogo);
@@ -224,8 +187,13 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (applet != null)
     {
-      String colour = applet.getParameter("defaultColour");
-
+      String colour = al.isNucleotide() ? applet
+              .getParameter("defaultColourNuc") : applet
+              .getParameter("defaultColourProt");
+      if (colour == null)
+      {
+        colour = applet.getParameter("defaultColour");
+      }
       if (colour == null)
       {
         colour = applet.getParameter("userDefinedColour");
@@ -255,16 +223,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   }
 
-  public void showSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
-
-  public boolean getShowSequenceFeatures()
-  {
-    return showSequenceFeatures;
-  }
-
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
    * row.
@@ -281,7 +239,7 @@ public class AlignViewport extends AlignmentViewport implements
     {
       return null;
     }
-    StringBuffer seqs = new StringBuffer();
+    StringBuilder seqs = new StringBuilder(consensus.annotations.length);
     for (int i = 0; i < consensus.annotations.length; i++)
     {
       if (consensus.annotations[i] != null)
@@ -302,64 +260,6 @@ public class AlignViewport extends AlignmentViewport implements
     return sq;
   }
 
-  public int getStartRes()
-  {
-    return startRes;
-  }
-
-  public int getEndRes()
-  {
-    return endRes;
-  }
-
-  public int getStartSeq()
-  {
-    return startSeq;
-  }
-
-  public void setStartRes(int res)
-  {
-    this.startRes = res;
-  }
-
-  public void setStartSeq(int seq)
-  {
-    this.startSeq = seq;
-  }
-
-  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;
-    }
-    if (res < 0)
-    {
-      res = 0;
-    }
-    this.endRes = res;
-  }
-
-  public void setEndSeq(int seq)
-  {
-    if (seq > alignment.getHeight())
-    {
-      seq = alignment.getHeight();
-    }
-    if (seq < 0)
-    {
-      seq = 0;
-    }
-    this.endSeq = seq;
-  }
-
-  public int getEndSeq()
-  {
-    return endSeq;
-  }
-
   java.awt.Frame nullFrame;
 
   protected FeatureSettings featureSettings = null;
@@ -377,13 +277,13 @@ public class AlignViewport extends AlignmentViewport implements
 
     java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
     setCharHeight((int) (heightScale * fm.getHeight()));
-    charWidth = (int) (widthScale * fm.charWidth('M'));
+    setCharWidth((int) (widthScale * fm.charWidth('M')));
 
-    if (upperCasebold)
+    if (isUpperCasebold())
     {
       Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
       fm = nullFrame.getGraphics().getFontMetrics(f2);
-      charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10));
+      setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
     }
   }
 
@@ -392,119 +292,6 @@ public class AlignViewport extends AlignmentViewport implements
     return font;
   }
 
-  public int getCharWidth()
-  {
-    return charWidth;
-  }
-
-  public void setCharHeight(int h)
-  {
-    this.charHeight = h;
-  }
-
-  public int getCharHeight()
-  {
-    return charHeight;
-  }
-
-  public void setWrappedWidth(int w)
-  {
-    this.wrappedWidth = w;
-  }
-
-  public int getwrappedWidth()
-  {
-    return wrappedWidth;
-  }
-
-  public AlignmentI getAlignment()
-  {
-    return alignment;
-  }
-
-  public void setAlignment(AlignmentI align)
-  {
-    this.alignment = align;
-  }
-
-  public void setWrapAlignment(boolean state)
-  {
-    wrapAlignment = state;
-  }
-
-  public void setShowText(boolean state)
-  {
-    showText = state;
-  }
-
-  public void setRenderGaps(boolean state)
-  {
-    renderGaps = state;
-  }
-
-  public boolean getColourText()
-  {
-    return showColourText;
-  }
-
-  public void setColourText(boolean state)
-  {
-    showColourText = state;
-  }
-
-  public void setShowBoxes(boolean state)
-  {
-    showBoxes = state;
-  }
-
-  public boolean getWrapAlignment()
-  {
-    return wrapAlignment;
-  }
-
-  public boolean getShowText()
-  {
-    return showText;
-  }
-
-  public boolean getShowBoxes()
-  {
-    return showBoxes;
-  }
-
-  public char getGapCharacter()
-  {
-    return getAlignment().getGapCharacter();
-  }
-
-  public void setGapCharacter(char gap)
-  {
-    if (getAlignment() != null)
-    {
-      getAlignment().setGapCharacter(gap);
-    }
-  }
-
-  public void setThreshold(int thresh)
-  {
-    threshold = thresh;
-  }
-
-  public int getThreshold()
-  {
-    return threshold;
-  }
-
-  public void setIncrement(int inc)
-  {
-    increment = inc;
-  }
-
-  public int getIncrement()
-  {
-    return increment;
-  }
-
   public void resetSeqLimits(int height)
   {
     setEndSeq(height / getCharHeight());
@@ -520,107 +307,6 @@ public class AlignViewport extends AlignmentViewport implements
     return currentTree;
   }
 
-  public boolean getShowJVSuffix()
-  {
-    return showJVSuffix;
-  }
-
-  public void setShowJVSuffix(boolean b)
-  {
-    showJVSuffix = 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;
-  }
-
-  public void setIgnoreGapsConsensus(boolean b)
-  {
-    ignoreGapsInConsensusCalculation = b;
-    updateConsensus(null);
-    if (globalColourScheme != null)
-    {
-      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-              ignoreGapsInConsensusCalculation);
-
-    }
-  }
-
-  public boolean getShowHiddenMarkers()
-  {
-    return showHiddenMarkers;
-  }
-
-  public void setShowHiddenMarkers(boolean show)
-  {
-    showHiddenMarkers = show;
-  }
-
-  public Color getSequenceColour(SequenceI seq)
-  {
-    if (sequenceColours == null || !sequenceColours.containsKey(seq))
-    {
-      return Color.white;
-    }
-    else
-    {
-      return (Color) sequenceColours.get(seq);
-    }
-  }
-
-  public void setSequenceColour(SequenceI seq, Color col)
-  {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
-
-    if (col == null)
-    {
-      sequenceColours.remove(seq);
-    }
-    else
-    {
-      sequenceColours.put(seq, col);
-    }
-  }
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
@@ -628,28 +314,6 @@ public class AlignViewport extends AlignmentViewport implements
     return centreColumnLabels;
   }
 
-  public void updateSequenceIdColours()
-  {
-
-    for (SequenceGroup sg : alignment.getGroups())
-    {
-      if (sg.idColour != null)
-      {
-        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
-        {
-          this.setSequenceColour(s, sg.idColour);
-        }
-      }
-    }
-  }
-
-  public boolean followHighlight = true;
-
-  public boolean getFollowHighlight()
-  {
-    return followHighlight;
-  }
-
   public boolean followSelection = true;
 
   /**
@@ -663,10 +327,22 @@ public class AlignViewport extends AlignmentViewport implements
 
   public void sendSelection()
   {
-    jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(applet).sendSelection(
-                    new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()), this);
+    getStructureSelectionManager().sendSelection(
+            new SequenceGroup(getSelectionGroup()),
+            new ColumnSelection(getColumnSelection()), this);
+  }
+
+  /**
+   * Returns an instance of the StructureSelectionManager scoped to this applet
+   * instance.
+   * 
+   * @return
+   */
+  @Override
+  public StructureSelectionManager getStructureSelectionManager()
+  {
+    return jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager(applet);
   }
 
   /**
@@ -702,12 +378,6 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
-  @Override
-  public boolean hasHiddenColumns()
-  {
-    return hasHiddenColumns;
-  }
-
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -727,4 +397,77 @@ public class AlignViewport extends AlignmentViewport implements
     return validCharWidth;
   }
 
+  public AnnotationColumnChooser getAnnotationColumnSelectionState()
+  {
+    return annotationColumnSelectionState;
+  }
+
+  public void setAnnotationColumnSelectionState(
+          AnnotationColumnChooser annotationColumnSelectionState)
+  {
+    this.annotationColumnSelectionState = annotationColumnSelectionState;
+  }
+
+  @Override
+  public void mirrorCommand(CommandI command, boolean undo,
+          StructureSelectionManager ssm, VamsasSource source)
+  {
+    // TODO refactor so this can be pulled up to superclass or controller
+    /*
+     * Do nothing unless we are a 'complement' of the source. May replace this
+     * with direct calls not via SSM.
+     */
+    if (source instanceof AlignViewportI
+            && ((AlignViewportI) source).getCodingComplement() == this)
+    {
+      // ok to continue;
+    }
+    else
+    {
+      return;
+    }
+
+    CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+            getGapCharacter());
+    if (mappedCommand != null)
+    {
+      mappedCommand.doCommand(null);
+      firePropertyChange("alignment", null, getAlignment().getSequences());
+
+      // ap.scalePanelHolder.repaint();
+      // ap.repaint();
+    }
+  }
+
+  @Override
+  public VamsasSource getVamsasSource()
+  {
+    return this;
+  }
+
+  /**
+   * If this viewport has a (Protein/cDNA) complement, then scroll the
+   * complementary alignment to match this one.
+   */
+  public void scrollComplementaryAlignment(AlignmentPanel complementPanel)
+  {
+    if (complementPanel == null)
+    {
+      return;
+    }
+
+    /*
+     * Populate a SearchResults object with the mapped location to scroll to. If
+     * there is no complement, or it is not following highlights, or no mapping
+     * is found, the result will be empty.
+     */
+    SearchResults sr = new SearchResults();
+    int seqOffset = findComplementScrollTarget(sr);
+    if (!sr.isEmpty())
+    {
+      complementPanel.setFollowingComplementScroll(true);
+      complementPanel.scrollToCentre(sr, seqOffset);
+    }
+  }
+
 }