X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=329f447fcc6eb6de89434be8bfdb6776ce6eefd9;hb=a8401d0452aac399083c1a89fb614adbfaa98ff8;hp=f8e1c5af7a3794d2a847cac4c951f37e0213e646;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index f8e1c5a..329f447 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,147 +1,185 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-public class SearchResults
-{
-
-  Match[] matches;
-
-  /**
-   * This method replaces the old search results which merely
-   * held an alignment index of search matches. This broke
-   * when sequences were moved around the alignment
-   * @param seq Sequence
-   * @param start int
-   * @param end int
-   */
-  public void addResult(SequenceI seq, int start, int end)
-  {
-    if (matches == null)
-    {
-      matches = new Match[]
-          {
-          new Match(seq, start, end)};
-      return;
-    }
-
-    int mSize = matches.length;
-
-    Match[] tmp = new Match[mSize + 1];
-    int m;
-    for (m = 0; m < mSize; m++)
-    {
-      tmp[m] = matches[m];
-    }
-
-    tmp[m] = new Match(seq, start, end);
-
-    matches = tmp;
-  }
-
-  /**
-   * This Method returns the search matches which lie between the
-   * start and end points of the sequence in question. It is
-   * optimised for returning objects for drawing on SequenceCanvas
-   */
-  public int[] getResults(SequenceI sequence, int start, int end)
-  {
-    if (matches == null)
-    {
-      return null;
-    }
-
-    int[] result = null;
-    int[] tmp = null;
-    int resultLength;
-
-    for (int m = 0; m < matches.length; m++)
-    {
-      if (matches[m].sequence == sequence)
-      {
-        int matchStart = matches[m].sequence.findIndex(matches[m].start) - 1;
-        int matchEnd = matches[m].sequence.findIndex(matches[m].end) - 1;
-
-        if (matchStart <= end && matchEnd >= start)
-        {
-          if (matchStart < start)
-          {
-            matchStart = start;
-          }
-
-          if (matchEnd > end)
-          {
-            matchEnd = end;
-          }
-
-          if (result == null)
-          {
-            result = new int[]
-                {
-                matchStart, matchEnd};
-          }
-          else
-          {
-            resultLength = result.length;
-            tmp = new int[resultLength + 2];
-            System.arraycopy(result, 0, tmp, 0, resultLength);
-            result = tmp;
-            result[resultLength] = matchStart;
-            result[resultLength + 1] = matchEnd;
-          }
-        }
-      }
-    }
-    return result;
-  }
-
-  public int getSize()
-  {
-    return matches == null ? 0 : matches.length;
-  }
-
-  public SequenceI getResultSequence(int index)
-  {
-    return matches[index].sequence;
-  }
-
-  public int getResultStart(int index)
-  {
-    return matches[index].start;
-  }
-
-  public int getResultEnd(int index)
-  {
-    return matches[index].end;
-  }
-
-  class Match
-  {
-    SequenceI sequence;
-    int start;
-    int end;
-
-    public Match(SequenceI seq, int start, int end)
-    {
-      sequence = seq;
-      this.start = start;
-      this.end = end;
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class SearchResults
+{
+
+  Match[] matches;
+
+  /**
+   * This method replaces the old search results which merely held an alignment
+   * index of search matches. This broke when sequences were moved around the
+   * alignment
+   * 
+   * @param seq
+   *                Sequence
+   * @param start
+   *                int
+   * @param end
+   *                int
+   */
+  public void addResult(SequenceI seq, int start, int end)
+  {
+    if (matches == null)
+    {
+      matches = new Match[]
+      { new Match(seq, start, end) };
+      return;
+    }
+
+    int mSize = matches.length;
+
+    Match[] tmp = new Match[mSize + 1];
+    int m;
+    for (m = 0; m < mSize; m++)
+    {
+      tmp[m] = matches[m];
+    }
+
+    tmp[m] = new Match(seq, start, end);
+
+    matches = tmp;
+  }
+  /**
+   * Quickly check if the given sequence is referred to in the search results
+   * @param sequence (specific alignment sequence or a dataset sequence)
+   * @return true if the results involve sequence
+   */
+  public boolean involvesSequence(SequenceI sequence)
+  {
+    if (matches==null || matches.length==0)
+    {
+      return false;
+    }
+    SequenceI ds = sequence.getDatasetSequence();
+    for (int m=0; m<matches.length; m++)
+    {
+      if (matches[m].sequence!=null &&
+              (matches[m].sequence==sequence 
+              || matches[m].sequence==ds))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+  /**
+   * This Method returns the search matches which lie between the start and end
+   * points of the sequence in question. It is optimised for returning objects
+   * for drawing on SequenceCanvas
+   */
+  public int[] getResults(SequenceI sequence, int start, int end)
+  {
+    if (matches == null)
+    {
+      return null;
+    }
+
+    int[] result = null;
+    int[] tmp = null;
+    int resultLength, matchStart = 0, matchEnd = 0;
+    boolean mfound;
+    for (int m = 0; m < matches.length; m++)
+    {
+      mfound = false;
+      if (matches[m].sequence == sequence)
+      {
+        mfound = true;
+        // locate aligned position
+        matchStart = sequence.findIndex(matches[m].start) - 1;
+        matchEnd = sequence.findIndex(matches[m].end) - 1;
+      }
+      else if (matches[m].sequence == sequence.getDatasetSequence())
+      {
+        mfound = true;
+        // locate region in local context
+        matchStart = sequence.findIndex(matches[m].start) - 1;
+        matchEnd = sequence.findIndex(matches[m].end) - 1;
+      }
+      if (mfound)
+      {
+        if (matchStart <= end && matchEnd >= start)
+        {
+          if (matchStart < start)
+          {
+            matchStart = start;
+          }
+
+          if (matchEnd > end)
+          {
+            matchEnd = end;
+          }
+
+          if (result == null)
+          {
+            result = new int[]
+            { matchStart, matchEnd };
+          }
+          else
+          {
+            resultLength = result.length;
+            tmp = new int[resultLength + 2];
+            System.arraycopy(result, 0, tmp, 0, resultLength);
+            result = tmp;
+            result[resultLength] = matchStart;
+            result[resultLength + 1] = matchEnd;
+          }
+        }
+      }
+    }
+    return result;
+  }
+
+  public int getSize()
+  {
+    return matches == null ? 0 : matches.length;
+  }
+
+  public SequenceI getResultSequence(int index)
+  {
+    return matches[index].sequence;
+  }
+
+  public int getResultStart(int index)
+  {
+    return matches[index].start;
+  }
+
+  public int getResultEnd(int index)
+  {
+    return matches[index].end;
+  }
+
+  class Match
+  {
+    SequenceI sequence;
+
+    int start;
+
+    int end;
+
+    public Match(SequenceI seq, int start, int end)
+    {
+      sequence = seq;
+      this.start = start;
+      this.end = end;
+    }
+  }
+}