X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=b088e0868acd7d1074be861dc08e357cb4b249c0;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=7294bae7b5d2fa957dfefe51f55c30eb5514ed14;hpb=0b9d0f8eba1cec46c0b31fdd402a826e26244ff5;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7294bae..b088e08 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
  */
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
@@ -35,29 +38,33 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.api.AlignCalcManagerI;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.OOMHandlerI;
-
-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.workers.AlignCalcManager;
-import jalview.workers.ConsensusThread;
-import jalview.workers.ConservationThread;
-import jalview.workers.StrucConsensusThread;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Stack;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -65,10 +72,9 @@ import jalview.workers.StrucConsensusThread;
  * @author $author$
  * @version $Revision: 1.141 $
  */
-public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI
+public class AlignViewport extends AlignmentViewport implements
+        SelectionSource, VamsasSource, AlignViewportI
 {
-  private static final int RIGHT_JUSTIFY = 1;
-
   int startRes;
 
   int endRes;
@@ -89,9 +95,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   boolean renderGaps = true;
 
-  boolean showSequenceFeatures = false;
-
-  boolean showAnnotation = true;
+  SequenceAnnotationOrder sortAnnotationsBy = null;
 
   int charHeight;
 
@@ -105,7 +109,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   boolean seqNameItalics;
 
-
   NJTree currentTree = null;
 
   boolean scaleAboveWrapped = false;
@@ -118,12 +121,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   boolean cursorMode = false;
 
-  /**
-   * Keys are the feature types which are currently visible. Note: Values are
-   * not used!
-   */
-  Hashtable featuresDisplayed = null;
-
   boolean antiAlias = false;
 
   Rectangle explodedPosition;
@@ -132,11 +129,9 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   boolean gatherViewsHere = false;
 
-  Stack historyList = new Stack();
-
-  Stack redoList = new Stack();
+  Stack<CommandI> historyList = new Stack<CommandI>();
 
-  Hashtable sequenceColours;
+  Stack<CommandI> redoList = new Stack<CommandI>();
 
   int thresholdTextColour = 0;
 
@@ -144,8 +139,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   Color textColour2 = Color.white;
 
-  boolean rightAlignIds = false;
-
+  private AnnotationColumnChooser annotationColumnSelectionState;
   /**
    * Creates a new AlignViewport object.
    * 
@@ -201,16 +195,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     setAlignment(al);
     if (hiddenColumns != null)
     {
-      this.colSel = hiddenColumns;
-      if (hiddenColumns.getHiddenColumns() != null
-              && hiddenColumns.getHiddenColumns().size() > 0)
-      {
-        hasHiddenColumns = true;
-      }
-      else
-      {
-        hasHiddenColumns = false;
-      }
+      colSel = hiddenColumns;
     }
     init();
   }
@@ -257,16 +242,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     setAlignment(al);
     if (hiddenColumns != null)
     {
-      this.colSel = hiddenColumns;
-      if (hiddenColumns.getHiddenColumns() != null
-              && hiddenColumns.getHiddenColumns().size() > 0)
-      {
-        hasHiddenColumns = true;
-      }
-      else
-      {
-        hasHiddenColumns = false;
-      }
+      colSel = hiddenColumns;
     }
     init();
   }
@@ -281,9 +257,9 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
     showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
-    showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+    setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
 
-    rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+    setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
     centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
     autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
@@ -319,21 +295,18 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     {
       if (!alignment.isNucleotide())
       {
-        showConservation=Cache.getDefault("SHOW_CONSERVATION", true);
-        showQuality=Cache.getDefault("SHOW_QUALITY", true);
+        showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
+        showQuality = Cache.getDefault("SHOW_QUALITY", true);
         showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
                 false);
-      } 
+      }
       showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
               true);
       showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
-      normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false);
+      normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+              false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
-      showConsensus=Cache.getDefault("SHOW_IDENTITY", true);
-      consensus = new AlignmentAnnotation("Consensus", "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      consensus.hasText = true;
-      consensus.autoCalculated = true;
+      showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
     }
     initAutoAnnotation();
     if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
@@ -354,28 +327,15 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
       }
     }
 
-    wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
-    showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
-            false);
-    sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
-    followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
-            true);
-  }
-
-  /**
-   * set the flag
-   * 
-   * @param b
-   *          features are displayed if true
-   */
-  public void setShowSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
-
-  public boolean getShowSequenceFeatures()
-  {
-    return showSequenceFeatures;
+    wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false);
+    showUnconserved = Cache.getDefault("SHOW_UNCONSERVED", false);
+    sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+    followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+    sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
+            Preferences.SORT_ANNOTATIONS,
+            SequenceAnnotationOrder.NONE.name()));
+    showAutocalculatedAbove = Cache.getDefault(
+            Preferences.SHOW_AUTOCALC_ABOVE, false);
   }
 
   /**
@@ -649,7 +609,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
               Desktop.instance).removeMappings(alignment.getCodonFrames());
     }
     this.alignment = align;
-    if (alignment!=null && alignment.getCodonFrames() != null)
+    if (alignment != null && alignment.getCodonFrames() != null)
     {
       StructureSelectionManager.getStructureSelectionManager(
               Desktop.instance).addMappings(alignment.getCodonFrames());
@@ -832,27 +792,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
    * 
    * @return DOCUMENT ME!
    */
-  public boolean getShowAnnotation()
-  {
-    return showAnnotation;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param b
-   *          DOCUMENT ME!
-   */
-  public void setShowAnnotation(boolean b)
-  {
-    showAnnotation = b;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
   public boolean getScaleAboveWrapped()
   {
     return scaleAboveWrapped;
@@ -911,7 +850,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     scaleRightWrapped = b;
   }
 
-
   public void setDataset(boolean b)
   {
     isDataset = b;
@@ -922,8 +860,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     return isDataset;
   }
 
-
-
   public boolean getShowHiddenMarkers()
   {
     return showHiddenMarkers;
@@ -934,35 +870,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     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);
-    }
-  }
-
   /**
    * returns the visible column regions of the alignment
    * 
@@ -995,9 +902,12 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
    */
   public long[] getUndoRedoHash()
   {
+    // TODO: JAL-1126
     if (historyList == null || redoList == null)
+    {
       return new long[]
       { -1, -1 };
+    }
     return new long[]
     { historyList.hashCode(), this.redoList.hashCode() };
   }
@@ -1043,24 +953,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     centreColumnLabels = centrecolumnlabels;
   }
 
-  public void updateSequenceIdColours()
-  {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
-    for (SequenceGroup sg:alignment.getGroups())
-    {
-      if (sg.idColour != null)
-      {
-        for (SequenceI s:sg.getSequences(getHiddenRepSequences()))
-        {
-          sequenceColours.put(s, sg.idColour);
-        }
-      }
-    }
-  }
-
   /**
    * enable or disable the display of Database Cross References in the sequence
    * ID tooltip
@@ -1099,23 +991,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     shownpfeats = show;
   }
 
-  /**
-   * 
-   * @return true if view has hidden rows
-   */
-  public boolean hasHiddenRows()
-  {
-    return hasHiddenRows;
-  }
-
-  /**
-   * 
-   * @return true if view has hidden columns
-   */
-  public boolean hasHiddenColumns()
-  {
-    return hasHiddenColumns;
-  }
 
   /**
    * when set, view will scroll to show the highlighted position
@@ -1143,8 +1018,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     return followSelection;
   }
 
-  boolean showSeqFeaturesHeight;
-
   public void sendSelection()
   {
     jalview.structure.StructureSelectionManager
@@ -1153,16 +1026,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
                     new ColumnSelection(getColumnSelection()), this);
   }
 
-  public void setShowSequenceFeaturesHeight(boolean selected)
-  {
-    showSeqFeaturesHeight = selected;
-  }
-
-  public boolean getShowSequenceFeaturesHeight()
-  {
-    return showSeqFeaturesHeight;
-  }
-
   /**
    * return the alignPanel containing the given viewport. Use this to get the
    * components currently handling the given viewport.
@@ -1252,7 +1115,9 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
         Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
                 .getPDBId();
         if (pdbs == null)
+        {
           continue;
+        }
         SequenceI sq;
         for (int p = 0; p < pdbs.size(); p++)
         {
@@ -1260,7 +1125,9 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
           if (p1.getId().equals(pdb.getId()))
           {
             if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+            {
               seqs.add(sq);
+            }
 
             continue;
           }
@@ -1271,7 +1138,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
 
-  
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -1282,13 +1148,65 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     normaliseSequenceLogo = state;
   }
 
-
   /**
    * 
-   * @return true if alignment characters should be displayed 
+   * @return true if alignment characters should be displayed
    */
   public boolean isValidCharWidth()
   {
     return validCharWidth;
   }
+
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+
+  private boolean showAutocalculatedAbove;
+
+  public AutoCalcSetting getCalcIdSettingsFor(String calcId)
+  {
+    return calcIdParams.get(calcId);
+  }
+
+  public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
+          boolean needsUpdate)
+  {
+    calcIdParams.put(calcId, settings);
+    // TODO: create a restart list to trigger any calculations that need to be
+    // restarted after load
+    // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
+    if (needsUpdate)
+    {
+      Cache.log.debug("trigger update for " + calcId);
+    }
+  }
+
+  protected SequenceAnnotationOrder getSortAnnotationsBy()
+  {
+    return sortAnnotationsBy;
+  }
+
+  protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+  {
+    this.sortAnnotationsBy = sortAnnotationsBy;
+  }
+
+  protected boolean isShowAutocalculatedAbove()
+  {
+    return showAutocalculatedAbove;
+  }
+
+  protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+  {
+    this.showAutocalculatedAbove = showAutocalculatedAbove;
+  }
+
+  public AnnotationColumnChooser getAnnotationColumnSelectionState()
+  {
+    return annotationColumnSelectionState;
+  }
+
+  public void setAnnotationColumnSelectionState(
+          AnnotationColumnChooser currentAnnotationColumnSelectionState)
+  {
+    this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
+  }
 }