X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=029280b2cb83657d8ec02f73598787d9d4652a19;hb=5964cc48187a5dbf0544f3058c09d553c845afa0;hp=f14ddd4a827d4baccc496903cdd7680c92a0b80f;hpb=a48744baf419c7c2cbbc548e7e7eb5098fd93b56;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index f14ddd4..029280b 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,18 +1,18 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
  * 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
+ * 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.
- *
- * 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
+ *  
+ * 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/>.
  */
 package jalview.viewmodel;
@@ -40,6 +40,7 @@ import jalview.workers.AlignCalcManager;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
+import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -48,9 +49,9 @@ import java.util.Vector;
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
- *
+ * 
  * @author jimp
- *
+ * 
  */
 public abstract class AlignmentViewport implements AlignViewportI
 {
@@ -95,8 +96,8 @@ public abstract class AlignmentViewport implements AlignViewportI
   }
 
   /**
-   *
-   *
+   * 
+   * 
    * @return flag indicating if colourchanges propagated to all groups
    */
   public boolean getColourAppliesToAllGroups()
@@ -108,7 +109,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * GUI state
-   *
+   * 
    * @return true if percent identity threshold is applied to shading
    */
   public boolean getAbovePIDThreshold()
@@ -118,8 +119,8 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * GUI state
-   *
-   *
+   * 
+   * 
    * @param b
    *          indicate if percent identity threshold is applied to shading
    */
@@ -132,7 +133,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param thresh
    *          DOCUMENT ME!
    */
@@ -143,7 +144,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getThreshold()
@@ -154,7 +155,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   int increment;
 
   /**
-   *
+   * 
    * @param inc
    *          set the scalar for bleaching colourschemes according to degree of
    *          conservation
@@ -166,7 +167,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * GUI State
-   *
+   * 
    * @return get scalar for bleaching colourschemes by conservation
    */
   public int getIncrement()
@@ -178,7 +179,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * GUI state
-   *
+   * 
    * @return true if conservation based shading is enabled
    */
   public boolean getConservationSelected()
@@ -188,7 +189,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * GUI state
-   *
+   * 
    * @param b
    *          enable conservation based shading
    */
@@ -371,8 +372,8 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       return;
     }
-    if (!calculator
-            .startRegisteredWorkersOfClass(jalview.workers.ConservationThread.class))
+    if (calculator
+            .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
     {
       calculator.registerWorker(new jalview.workers.ConservationThread(
               this, ap));
@@ -389,7 +390,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       return;
     }
-    if (!calculator.startRegisteredWorkersOfClass(ConsensusThread.class))
+    if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
     {
       calculator.registerWorker(new ConsensusThread(this, ap));
     }
@@ -409,8 +410,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       return;
     }
-    if (!calculator
-            .startRegisteredWorkersOfClass(StrucConsensusThread.class))
+    if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
     {
       calculator.registerWorker(new StrucConsensusThread(this, ap));
     }
@@ -544,7 +544,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   }
 
   /**
-   *
+   * 
    * @return flag to indicate if the consensus histogram should be rendered by
    *         default
    */
@@ -589,8 +589,8 @@ public abstract class AlignmentViewport implements AlignViewportI
   }
 
   /**
-   *
-   *
+   * 
+   * 
    * @return null or the currently selected sequence region
    */
   public SequenceGroup getSelectionGroup()
@@ -600,10 +600,10 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * Set the selection group for this window.
-   *
+   * 
    * @param sg
    *          - group holding references to sequences in this alignment view
-   *
+   * 
    */
   public void setSelectionGroup(SequenceGroup sg)
   {
@@ -631,7 +631,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   }
 
   /**
-   *
+   * 
    * @return
    */
   @Override
@@ -685,7 +685,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * unique viewId for synchronizing state (e.g. with stored Jalview Project)
-   *
+   * 
    */
   protected String viewId = null;
 
@@ -718,10 +718,10 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * checks current SelectionGroup against record of last hash value, and
    * updates record.
-   *
+   * 
    * @param b
    *          update the record of last hash value
-   *
+   * 
    * @return true if SelectionGroup changed since last call (when b is true)
    */
   public boolean isSelectionGroupChanged(boolean b)
@@ -742,7 +742,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * checks current colsel against record of last hash value, and optionally
    * updates record.
-   *
+   * 
    * @param b
    *          update the record of last hash value
    * @return true if colsel changed since last call (when b is true)
@@ -782,7 +782,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * Property change listener for changes in alignment
-   *
+   * 
    * @param listener
    *          DOCUMENT ME!
    */
@@ -794,7 +794,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param listener
    *          DOCUMENT ME!
    */
@@ -806,7 +806,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * Property change listener for changes in alignment
-   *
+   * 
    * @param prop
    *          DOCUMENT ME!
    * @param oldvalue
@@ -1014,7 +1014,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * This method returns an array of new SequenceI objects derived from the
    * whole alignment or just the current selection with start and end points
    * adjusted
-   *
+   * 
    * @note if you need references to the actual SequenceI objects in the
    *       alignment or currently selected then use getSequenceSelection()
    * @return selection as new sequenceI objects
@@ -1027,7 +1027,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     // JBPNote: in applet, this method returned references to the alignment
     // sequences, and it did not honour the presence/absence of annotation
     // attached to the alignment (probably!)
-    if (selectionGroup == null)
+    if (selectionGroup == null || selectionGroup.getSize() == 0)
     {
       sequences = alignment.getSequencesArray();
       AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
@@ -1050,7 +1050,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * get the currently selected sequence objects or all the sequences in the
    * alignment.
-   *
+   * 
    * @return array of references to sequence objects
    */
   public SequenceI[] getSequenceSelection()
@@ -1072,7 +1072,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * if columns are hidden they will not be returned in the result. Use this for
    * calculating trees, PCA, redundancy etc on views which contain hidden
    * columns.
-   *
+   * 
    * @return String[]
    */
   public jalview.datamodel.CigarArray getViewAsCigars(
@@ -1086,7 +1086,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * return a compact representation of the current alignment selection to pass
    * to an analysis function
-   *
+   * 
    * @param selectedOnly
    *          boolean true to just return the selected view
    * @return AlignmentView
@@ -1100,7 +1100,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * return a compact representation of the current alignment selection to pass
    * to an analysis function
-   *
+   * 
    * @param selectedOnly
    *          boolean true to just return the selected view
    * @param markGroups
@@ -1121,7 +1121,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * if columns are hidden they will not be returned in the result. Use this for
    * calculating trees, PCA, redundancy etc on views which contain hidden
    * columns.
-   *
+   * 
    * @return String[]
    */
   public String[] getViewAsString(boolean selectedRegionOnly)
@@ -1162,7 +1162,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   /**
    * return visible region boundaries within given column range
-   *
+   * 
    * @param min
    *          first column (inclusive, from 0)
    * @param max
@@ -1233,7 +1233,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * apply any post-edit constraints and trigger any calculations needed after
    * an edit has been performed on the alignment
-   *
+   * 
    * @param ap
    */
   public void alignmentChanged(AlignmentViewPanel ap)
@@ -1374,4 +1374,146 @@ public abstract class AlignmentViewport implements AlignViewportI
     }
   }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.api.AlignViewportI#calcPanelHeight()
+   */
+  public int calcPanelHeight()
+  {
+    // setHeight of panels
+    AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation();
+    int height = 0;
+    int charHeight = getCharHeight();
+    if (aa != null)
+    {
+      boolean graphgrp[] = null;
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (aa[i] == null)
+        {
+          System.err.println("Null annotation row: ignoring.");
+          continue;
+        }
+        if (!aa[i].visible)
+        {
+          continue;
+        }
+        if (aa[i].graphGroup > -1)
+        {
+          if (graphgrp == null)
+          {
+            graphgrp = new boolean[aa.length];
+          }
+          if (graphgrp[aa[i].graphGroup])
+          {
+            continue;
+          }
+          else
+          {
+            graphgrp[aa[i].graphGroup] = true;
+          }
+        }
+        aa[i].height = 0;
+
+        if (aa[i].hasText)
+        {
+          aa[i].height += charHeight;
+        }
+
+        if (aa[i].hasIcons)
+        {
+          aa[i].height += 16;
+        }
+
+        if (aa[i].graph > 0)
+        {
+          aa[i].height += aa[i].graphHeight;
+        }
+
+        if (aa[i].height == 0)
+        {
+          aa[i].height = 20;
+        }
+
+        height += aa[i].height;
+      }
+    }
+    if (height == 0)
+    {
+      // set minimum
+      height = 20;
+    }
+    return height;
+  }
+
+  @Override
+  public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
+          boolean preserveNewGroupSettings)
+  {
+    boolean updateCalcs = false;
+    boolean conv = isShowGroupConservation();
+    boolean cons = isShowGroupConsensus();
+    boolean showprf = isShowSequenceLogo();
+    boolean showConsHist = isShowConsensusHistogram();
+    boolean normLogo = isNormaliseSequenceLogo();
+
+    /**
+     * TODO reorder the annotation rows according to group/sequence ordering on
+     * alignment
+     */
+    boolean sortg = true;
+
+    // remove old automatic annotation
+    // add any new annotation
+
+    // intersect alignment annotation with alignment groups
+
+    AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
+    List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+    if (aan != null)
+    {
+      for (int an = 0; an < aan.length; an++)
+      {
+        if (aan[an].autoCalculated && aan[an].groupRef != null)
+        {
+          oldrfs.add(aan[an].groupRef);
+          alignment.deleteAnnotation(aan[an]);
+          aan[an] = null;
+        }
+      }
+    }
+    if (alignment.getGroups() != null)
+    {
+      for (SequenceGroup sg : alignment.getGroups())
+      {
+        updateCalcs = false;
+        if (applyGlobalSettings
+                || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
+        {
+          // set defaults for this group's conservation/consensus
+          sg.setshowSequenceLogo(showprf);
+          sg.setShowConsensusHistogram(showConsHist);
+          sg.setNormaliseSequenceLogo(normLogo);
+        }
+        if (conv)
+        {
+          updateCalcs = true;
+          alignment.addAnnotation(sg.getConservationRow(), 0);
+        }
+        if (cons)
+        {
+          updateCalcs = true;
+          alignment.addAnnotation(sg.getConsensus(), 0);
+        }
+        // refresh the annotation rows
+        if (updateCalcs)
+        {
+          sg.recalcConservation();
+        }
+      }
+    }
+    oldrfs.clear();
+  }
+
 }