X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=3bf7bc4168b4e676ef38b7c598170c404583bb87;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=8ece1e5f7615023a3a136e320d6a13c9707eadb0;hpb=60ee9fb76ea07566ece5c3455a1abedfff467354;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 8ece1e5..3bf7bc4 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -30,6 +30,7 @@ import java.awt.Color;
 import java.beans.PropertyChangeListener;
 import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 
@@ -87,7 +88,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * group members
    */
-  private List<SequenceI> sequences = new ArrayList<>();
+  private List<SequenceI> sequences;
 
   /**
    * representative sequence for this group (if any)
@@ -101,11 +102,15 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public ResidueShaderI cs;
 
-  // start column (base 0)
-  int startRes = 0;
+  /**
+   * start column (base 0)
+   */
+  private int startRes = 0;
 
-  // end column (base 0)
-  int endRes = 0;
+  /**
+   *  end column (base 0)
+   */
+  private int endRes = 0;
 
   public Color outlineColour = Color.black;
 
@@ -157,6 +162,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     groupName = "JGroup:" + this.hashCode();
     cs = new ResidueShader();
+    sequences = new ArrayList<>();
   }
 
   /**
@@ -208,6 +214,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       displayBoxes = seqsel.displayBoxes;
       displayText = seqsel.displayText;
       colourText = seqsel.colourText;
+      
       startRes = seqsel.startRes;
       endRes = seqsel.endRes;
       cs = new ResidueShader((ResidueShader) seqsel.cs);
@@ -237,6 +244,17 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
+  /**
+   * Constructor that copies the given list of sequences
+   * 
+   * @param seqs
+   */
+  public SequenceGroup(List<SequenceI> seqs)
+  {
+    this();
+    this.sequences.addAll(seqs);
+  }
+
   public boolean isShowSequenceLogo()
   {
     return showSequenceLogo;
@@ -644,8 +662,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     conservation.description = "Conservation for group " + getName()
             + " less than " + consPercGaps + "% gaps";
     // preserve width if already set
-    int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
-            : endRes + 1)
+    int aWidth = (conservation.annotations != null)
+            ? (endRes < conservation.annotations.length
+                    ? conservation.annotations.length
+                    : endRes + 1)
             : endRes + 1;
     conservation.annotations = null;
     conservation.annotations = new Annotation[aWidth]; // should be alignment
@@ -665,8 +685,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     consensus.description = "Percent Identity";
     consensusData = cnsns;
     // preserve width if already set
-    int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
-            : endRes + 1)
+    int aWidth = (consensus.annotations != null)
+            ? (endRes < consensus.annotations.length
+                    ? consensus.annotations.length
+                    : endRes + 1)
             : endRes + 1;
     consensus.annotations = null;
     consensus.annotations = new Annotation[aWidth]; // should be alignment width
@@ -712,7 +734,6 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
-      List<SequenceI> before = sequences;
       sequences.remove(s);
       changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
               sequences.size() + 1, sequences.size());
@@ -748,13 +769,16 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * Set the first column selected by this group. Runs from 0<=i<N_cols
    * 
-   * @param i
+   * @param newStart
    */
-  public void setStartRes(int i)
+  public void setStartRes(int newStart)
   {
     int before = startRes;
-    startRes = i;
-    changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+   startRes= Math.max(0,newStart); // sanity check for negative start column positions
+   changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+    
+
+
   }
 
   /**
@@ -1185,9 +1209,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       if (consensus.annotations[i] != null)
       {
-        if (consensus.annotations[i].description.charAt(0) == '[')
+        String desc = consensus.annotations[i].description;
+        if (desc.length() > 1 && desc.charAt(0) == '[')
         {
-          seqs.append(consensus.annotations[i].description.charAt(1));
+          seqs.append(desc.charAt(1));
         }
         else
         {
@@ -1313,38 +1338,16 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<>();
-    if (calcId == null)
-    {
-      return aa;
-    }
-    for (AlignmentAnnotation a : getAlignmentAnnotation())
-    {
-      if (calcId.equals(a.getCalcId()))
-      {
-        aa.add(a);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotation(
+            Arrays.asList(getAlignmentAnnotation()), calcId);
   }
 
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
-    for (AlignmentAnnotation ann : getAlignmentAnnotation())
-    {
-      if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
-              .equals(calcId)))
-              && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
-              && (label == null || (ann.label != null && ann.label
-                      .equals(label))))
-      {
-        aa.add(ann);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotations(
+            Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
   }
 
   /**
@@ -1355,17 +1358,8 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public boolean hasAnnotation(String calcId)
   {
-    if (calcId != null && !"".equals(calcId))
-    {
-      for (AlignmentAnnotation a : getAlignmentAnnotation())
-      {
-        if (a.getCalcId() == calcId)
-        {
-          return true;
-        }
-      }
-    }
-    return false;
+    return AlignmentAnnotation
+            .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId);
   }
 
   /**
@@ -1375,10 +1369,10 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
-      List<SequenceI> before = sequences;
+      int before = sequences.size();
       sequences.clear();
       changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
-              sequences);
+              sequences.size());
     }
   }
 
@@ -1466,7 +1460,8 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public boolean isNucleotide()
   {
-    if (context != null) {
+    if (context != null)
+    {
       return context.isNucleotide();
     }
     return false;