X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=3bf7bc4168b4e676ef38b7c598170c404583bb87;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=20b23a9a0365fd60766b2d1ae099bf52d6099032;hpb=7f964795c092e1bf4fbee18904b3d3dc1c29ddf8;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 20b23a9..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<>();
   }
 
   /**
@@ -184,19 +190,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     this.displayText = displayText;
     this.colourText = colourText;
     this.cs = new ResidueShader(scheme);
-    
-    if (start > 0) // sanity check for negative start column positions
-    {
-      startRes = start;
-    }
-    else
-    {
-      jalview.bin.Cache.log.warn(
-              "Negative start column index detected, resetting to default index: "
-                      + startRes);
-      // start = startRes;
-    }
-    
+    startRes = start;
     endRes = end;
     recalcConservation();
   }
@@ -221,19 +215,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       displayText = seqsel.displayText;
       colourText = seqsel.colourText;
       
-      if (seqsel.startRes > 0) // sanity check for negative start column
-                               // positions
-      {
-        startRes = seqsel.startRes;
-      }
-      else
-      {
-        jalview.bin.Cache.log.warn(
-                "Negative start column index detected, resetting to default index: "
-                        + startRes);
-        // seqsel.startRes = startRes;
-      }
-  
+      startRes = seqsel.startRes;
       endRes = seqsel.endRes;
       cs = new ResidueShader((ResidueShader) seqsel.cs);
       if (seqsel.description != null)
@@ -262,6 +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;
@@ -776,13 +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);
+    
+
+
   }
 
   /**
@@ -1213,9 +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
         {
@@ -1341,39 +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);
   }
 
   /**
@@ -1384,17 +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);
   }
 
   /**