X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fpacked%2FJalviewDataset.java;h=c1ca1b7a28765621332c821cd6c0f7f772f29a87;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=95de89d6376b81e526ab6b6d34a67adf94028f16;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/io/packed/JalviewDataset.java b/src/jalview/io/packed/JalviewDataset.java
index 95de89d..c1ca1b7 100644
--- a/src/jalview/io/packed/JalviewDataset.java
+++ b/src/jalview/io/packed/JalviewDataset.java
@@ -1,29 +1,35 @@
-/*******************************************************************************
- * 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.
+ */
 package jalview.io.packed;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.io.NewickFile;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 public class JalviewDataset
 {
@@ -39,27 +45,33 @@ public class JalviewDataset
   {
     return parentDataset;
   }
+
   /**
-   * @param parentDataset the parentDataset to set
+   * @param parentDataset
+   *          the parentDataset to set
    */
   public void setParentDataset(AlignmentI parentDataset)
   {
     this.parentDataset = parentDataset;
   }
+
   /**
    * @return the featureColours
    */
-  public Hashtable getFeatureColours()
+  public Map<String, FeatureColourI> getFeatureColours()
   {
     return featureColours;
   }
+
   /**
-   * @param featureColours the featureColours to set
+   * @param featureColours
+   *          the featureColours to set
    */
-  public void setFeatureColours(Hashtable featureColours)
+  public void setFeatureColours(Map<String, FeatureColourI> featureColours)
   {
     this.featureColours = featureColours;
   }
+
   /**
    * @return the seqDetails
    */
@@ -67,88 +79,106 @@ public class JalviewDataset
   {
     return seqDetails;
   }
+
   /**
-   * @param seqDetails the seqDetails to set
+   * @param seqDetails
+   *          the seqDetails to set
    */
   public void setSeqDetails(Hashtable seqDetails)
   {
     this.seqDetails = seqDetails;
   }
+
   /**
    * @return the al
    */
   public List<AlignmentSet> getAl()
   {
-    return (al==null) ? new ArrayList<AlignmentSet>() : al;
+    return (al == null) ? new ArrayList<AlignmentSet>() : al;
   }
+
   /**
    * current alignment being worked on.
    */
   List<AlignmentSet> al;
-  public class AlignmentSet {
+
+  public class AlignmentSet
+  {
     public AlignmentI al;
+
     public List<jalview.io.NewickFile> trees;
-    AlignmentSet(AlignmentI a) {
+
+    AlignmentSet(AlignmentI a)
+    {
       al = a;
       trees = new ArrayList<jalview.io.NewickFile>();
     }
+
     /**
      * deuniquify the current alignment in the context, merging any new
      * annotation/features with the existing set
      * 
      * @param context
      */
-      void deuniquifyAlignment()
+    void deuniquifyAlignment()
+    {
+      if (seqDetails == null || seqDetails.size() == 0)
       {
-        if (seqDetails==null || seqDetails.size()==0)
-        {
-          // nothing to do
-          return;
-        }
-        // 1. recover correct names and attributes for each sequence in alignment.
-        /*
-         * TODO: housekeeping w.r.t. recovery of dataset and annotation
-         * references for input sequences, and then dataset sequence creation
-         * for new sequences retrieved from service // finally, attempt to
-         * de-uniquify to recover input sequence identity, and try to map back
-         * onto dataset Note: this
-         * jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true); will
-         * NOT WORK - the returned alignment may contain multiple versions of
-         * the input sequence, each being a subsequence of the original.
-         * deuniquify also removes existing annotation and features added in the
-         * previous step... al.setDataset(dataset); // add in new sequences
-         * retrieved from sequence search which are not already in dataset. //
-         * trigger a 'fetchDBids' to annotate sequences with database ids...
-         */
-        //jalview.analysis.SeqsetUtils.deuniquifyAndMerge(parentDataset, seqDetails, al,true);
-        
-        jalview.analysis.SeqsetUtils.deuniquify(seqDetails, al.getSequencesArray(),true);
-        // 2. Update names of associated nodes in any trees
-        for (NewickFile nf:trees)
-        {
-          // the following works because all trees are already had node/SequenceI associations created.
-          jalview.analysis.NJTree njt = new jalview.analysis.NJTree(al.getSequencesArray(), nf);
-          // this just updates the displayed leaf name on the tree according to the SequenceIs.
-          njt.renameAssociatedNodes();
-        }
-        
+        // nothing to do
+        return;
       }
-      /**
-       * set modification flag. If anything modifies the alignment in the current set, this flag should be true
+      // 1. recover correct names and attributes for each sequence in alignment.
+      /*
+       * TODO: housekeeping w.r.t. recovery of dataset and annotation references
+       * for input sequences, and then dataset sequence creation for new
+       * sequences retrieved from service // finally, attempt to de-uniquify to
+       * recover input sequence identity, and try to map back onto dataset Note:
+       * this jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true);
+       * will NOT WORK - the returned alignment may contain multiple versions of
+       * the input sequence, each being a subsequence of the original.
+       * deuniquify also removes existing annotation and features added in the
+       * previous step... al.setDataset(dataset); // add in new sequences
+       * retrieved from sequence search which are not already in dataset. //
+       * trigger a 'fetchDBids' to annotate sequences with database ids...
        */
-      private boolean modified=false;
-      
-      /**
-       * @return the modified
-       */
-      public boolean isModified()
+      // jalview.analysis.SeqsetUtils.deuniquifyAndMerge(parentDataset,
+      // seqDetails, al,true);
+
+      jalview.analysis.SeqsetUtils.deuniquify(seqDetails,
+              al.getSequencesArray(), true);
+      // 2. Update names of associated nodes in any trees
+      for (NewickFile nf : trees)
       {
-        return modified;
+        // the following works because all trees are already had node/SequenceI
+        // associations created.
+        jalview.analysis.NJTree njt = new jalview.analysis.NJTree(
+                al.getSequencesArray(), nf);
+        // this just updates the displayed leaf name on the tree according to
+        // the SequenceIs.
+        njt.renameAssociatedNodes();
       }
-      /**
-       * or the modification state with the given state 
-       * @param modifiedFromAction
-       */
+
+    }
+
+    /**
+     * set modification flag. If anything modifies the alignment in the current
+     * set, this flag should be true
+     */
+    private boolean modified = false;
+
+    /**
+     * @return the modified
+     */
+    public boolean isModified()
+    {
+      return modified;
+    }
+
+    /**
+     * or the modification state with the given state
+     * 
+     * @param modifiedFromAction
+     */
     public void updateSetModified(boolean modifiedFromAction)
     {
       modified |= modifiedFromAction;
@@ -158,115 +188,143 @@ public class JalviewDataset
   /**
    * current set of feature colours
    */
-  Hashtable featureColours;
+  Map<String, FeatureColourI> featureColours;
 
   /**
    * original identity of each sequence in results
    */
   Hashtable seqDetails;
 
-  public boolean relaxedIdMatching=false;
+  public boolean relaxedIdMatching = false;
 
   public JalviewDataset()
   {
     seqDetails = new Hashtable();
     al = new ArrayList<AlignmentSet>();
     parentDataset = null;
-    featureColours = new Hashtable();
+    featureColours = new HashMap<String, FeatureColourI>();
   }
+
   /**
    * context created from an existing alignment.
+   * 
    * @param parentAlignment
    */
-  public JalviewDataset(AlignmentI aldataset, Hashtable fc, Hashtable seqDets)
+  public JalviewDataset(AlignmentI aldataset,
+          Map<String, FeatureColourI> fc, Hashtable seqDets)
   {
+    // TODO not used - remove?
     this(aldataset, fc, seqDets, null);
   }
+
   /**
    * 
-   * @param aldataset - parent dataset for any new alignment/sequence data (must not be null)
-   * @param fc  (may be null) feature settings for the alignment where new feature renderstyles are stored
-   * @param seqDets - (may be null) anonymised sequence information created by Sequence uniquifier 
-   * @param parentAlignment (may be null) alignment to associate new annotation and trees with.
+   * @param aldataset
+   *          - parent dataset for any new alignment/sequence data (must not be
+   *          null)
+   * @param fc
+   *          (may be null) feature settings for the alignment where new feature
+   *          renderstyles are stored
+   * @param seqDets
+   *          - (may be null) anonymised sequence information created by
+   *          Sequence uniquifier
+   * @param parentAlignment
+   *          (may be null) alignment to associate new annotation and trees
+   *          with.
    */
-  public JalviewDataset(AlignmentI aldataset, Hashtable fc, Hashtable seqDets, AlignmentI parentAlignment)
+  public JalviewDataset(AlignmentI aldataset,
+          Map<String, FeatureColourI> fc, Hashtable seqDets,
+          AlignmentI parentAlignment)
   {
     this();
     parentDataset = aldataset;
-    if (parentAlignment!=null)
+    if (parentAlignment != null)
     {
       parentDataset = parentAlignment.getDataset();
-      if (parentDataset==null)
+      if (parentDataset == null)
       {
         parentDataset = parentAlignment;
-      } else {
+      }
+      else
+      {
         addAlignment(parentAlignment);
       }
     }
-    if (seqDets!=null)
+    if (seqDets != null)
     {
       seqDetails = seqDets;
     }
-    if (fc!=null)
+    if (fc != null)
     {
       featureColours = fc;
     }
-    
-    
+
   }
 
   public boolean hasAlignments()
   {
-    return al!=null && al.size()>0;
+    return al != null && al.size() > 0;
   }
 
   public AlignmentI getLastAlignment()
   {
-    return (al==null || al.size()<1) ? null: al.get(al.size()-1).al;
+    return (al == null || al.size() < 1) ? null : al.get(al.size() - 1).al;
   }
+
   public AlignmentSet getLastAlignmentSet()
   {
-    return (al==null || al.size()<1) ? null: al.get(al.size()-1);
+    return (al == null || al.size() < 1) ? null : al.get(al.size() - 1);
   }
 
   /**
-   * post process (deuniquify) the current alignment and its dependent data, and then add newal to the dataset.
+   * post process (deuniquify) the current alignment and its dependent data, and
+   * then add newal to the dataset.
+   * 
    * @param newal
    */
-public void addAlignment(AlignmentI newal) {
-  if (!hasAlignments())
+  public void addAlignment(AlignmentI newal)
   {
-    al = new ArrayList<AlignmentSet>();
-  } 
-  AlignmentSet last = getLastAlignmentSet();
-  if (last!=null) {
-    System.err.println("Deuniquifying last alignment set.");
-    last.deuniquifyAlignment();
+    if (!hasAlignments())
+    {
+      al = new ArrayList<AlignmentSet>();
+    }
+    AlignmentSet last = getLastAlignmentSet();
+    if (last != null)
+    {
+      System.err.println("Deuniquifying last alignment set.");
+      last.deuniquifyAlignment();
+    }
+    al.add(new AlignmentSet(newal));
   }
-  al.add(new AlignmentSet(newal));
-}
 
-public void addTreeFromFile(NewickFile nf)
-{
-  AlignmentSet lal = getLastAlignmentSet();
-  lal.trees.add(nf);
-}
+  public void addTreeFromFile(NewickFile nf)
+  {
+    AlignmentSet lal = getLastAlignmentSet();
+    lal.trees.add(nf);
+  }
 
-public boolean hasSequenceAssoc()
-{
-  // TODO: discover where sequence associated data should be put.
-  return false;
-}
-public SequenceI getLastAssociatedSequence() {
-  // TODO: delineate semantics for associating uniquified data with potentially de-uniquified sequence.
-  return null;
-}
-/**
- * update the modified state flag for the current set with the given modification state
- * @param modified - this will be ored with current modification state
- */
-public void updateSetModified(boolean modified)
-{
-  getLastAlignmentSet().updateSetModified(modified);
+  public boolean hasSequenceAssoc()
+  {
+    // TODO: discover where sequence associated data should be put.
+    return false;
+  }
+
+  public SequenceI getLastAssociatedSequence()
+  {
+    // TODO: delineate semantics for associating uniquified data with
+    // potentially de-uniquified sequence.
+    return null;
+  }
+
+  /**
+   * update the modified state flag for the current set with the given
+   * modification state
+   * 
+   * @param modified
+   *          - this will be ored with current modification state
+   */
+  public void updateSetModified(boolean modified)
+  {
+    getLastAlignmentSet().updateSetModified(modified);
+  }
 }
-}
\ No newline at end of file