remove gaps method from AlignFrame.remove_gaps_actionPerformed

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 0225c88..dd2517c 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -718,4 +718,61 @@ public class Sequence implements SequenceI
     return getSubSequence(start, getLength());
   }
 
+  public int removeGaps() {
+    if (sequence!=null)
+      return removeGaps(0, getLength());
+    return 0;
+  }
+
+  public int removeGaps(int start, int end) {
+    int jSize = getLength();
+    int oSize=jSize;
+    if (jSize<=start)
+      return 0;
+    if (end>jSize)
+      end = jSize;
+
+    // Removing a range is much quicker than removing gaps
+    // one by one for long sequences
+    int j = start;
+    int rangeStart=-1, rangeEnd=-1;
+
+    do
+    {
+      if (jalview.util.Comparison.isGap(getCharAt(j)))
+      {
+        if(rangeStart==-1)
+         {
+           rangeStart = j;
+           rangeEnd = j+1;
+         }
+         else
+         {
+           rangeEnd++;
+         }
+         j++;
+      }
+      else
+      {
+        if(rangeStart>-1)
+        {
+          deleteChars(rangeStart, rangeEnd);
+          j-=rangeEnd-rangeStart;
+          jSize-=rangeEnd-rangeStart;
+          rangeStart = -1;
+          rangeEnd = -1;
+        }
+        else
+          j++;
+      }
+    }
+    while (j < end && j < jSize);
+    if(rangeStart>-1)
+    {
+     deleteChars(rangeStart, rangeEnd);
+     jSize-=rangeEnd-rangeStart;
+    }
+    return oSize-jSize; // number of deleted characters.
+  }
+
 }

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 0842d94..6c9fa2a 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,274 +1,286 @@
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public interface SequenceI\r
-{\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param name DOCUMENT ME!\r
-     */\r
-    public void setName(String name);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public String getName();\r
-\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param start DOCUMENT ME!\r
-     */\r
-    public void setStart(int start);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int getStart();\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public String getDisplayId(boolean jvsuffix);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param end DOCUMENT ME!\r
-     */\r
-    public void setEnd(int end);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int getEnd();\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int getLength();\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param sequence DOCUMENT ME!\r
-     */\r
-    public void setSequence(String sequence);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public String getSequence();\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param start DOCUMENT ME!\r
-     * @param end DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public String getSequence(int start, int end);\r
-    /**\r
-     * create a new sequence object from start to end of this sequence\r
-     * @param start int\r
-     * @param end int\r
-     * @return SequenceI\r
-     */\r
-    public SequenceI getSubSequence(int start, int end);\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param i DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public char getCharAt(int i);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param desc DOCUMENT ME!\r
-     */\r
-    public void setDescription(String desc);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public String getDescription();\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param pos DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int findIndex(int pos);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param i DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int findPosition(int i);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int[] gapMap();\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param i DOCUMENT ME!\r
-     * @param j DOCUMENT ME!\r
-     */\r
-    public void deleteChars(int i, int j);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param i DOCUMENT ME!\r
-     */\r
-    public void deleteCharAt(int i);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param i DOCUMENT ME!\r
-     * @param c DOCUMENT ME!\r
-     */\r
-    public void insertCharAt(int i, char c);\r
-\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param c DOCUMENT ME!\r
-     */\r
-    public void setColor(Color c);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public Color getColor();\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public SequenceFeature[] getSequenceFeatures();\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param v DOCUMENT ME!\r
-     */\r
-    public void setSequenceFeatures(SequenceFeature [] features);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param id DOCUMENT ME!\r
-     */\r
-    public void setPDBId(Vector ids);\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public Vector getPDBId();\r
-\r
-    public void addPDBId(PDBEntry entry);\r
-\r
-    public String getVamsasId();\r
-\r
-    public void setVamsasId(String id);\r
-\r
-    public void setDBRef(DBRefEntry[] dbs);\r
-\r
-    public DBRefEntry [] getDBRef();\r
-\r
-    public void addDBRef(DBRefEntry entry);\r
-\r
-    public void addSequenceFeature(SequenceFeature sf);\r
-\r
-    public void setDatasetSequence(SequenceI seq);\r
-\r
-    public SequenceI getDatasetSequence();\r
-\r
-    public AlignmentAnnotation [] getAnnotation();\r
-\r
-    public void addAlignmentAnnotation(AlignmentAnnotation annotation);\r
-\r
-    public SequenceGroup getHiddenSequences();\r
-\r
-    public void addHiddenSequence(SequenceI seq);\r
-\r
-    public void showHiddenSequence(SequenceI seq);\r
-\r
-    public void changeCase(boolean toUpper, int start, int end);\r
-\r
-    public void toggleCase(int start, int end);\r
-\r
-  /**\r
-   * getSubSequence from start to end of sequence\r
-   * @param start first residue in subSequence\r
-   * @return SequenceI\r
-   */\r
-  public SequenceI getSubSequence(int start);\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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;
+
+import java.util.*;
+
+import java.awt.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public interface SequenceI
+{
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName();
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     */
+    public void setStart(int start);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStart();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDisplayId(boolean jvsuffix);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param end DOCUMENT ME!
+     */
+    public void setEnd(int end);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEnd();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getLength();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sequence DOCUMENT ME!
+     */
+    public void setSequence(String sequence);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getSequence();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getSequence(int start, int end);
+    /**
+     * create a new sequence object from start to end of this sequence
+     * @param start int
+     * @param end int
+     * @return SequenceI
+     */
+    public SequenceI getSubSequence(int start, int end);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char getCharAt(int i);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param desc DOCUMENT ME!
+     */
+    public void setDescription(String desc);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDescription();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pos DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int findIndex(int pos);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int findPosition(int i);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int[] gapMap();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     */
+    public void deleteChars(int i, int j);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void deleteCharAt(int i);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     */
+    public void insertCharAt(int i, char c);
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setColor(Color c);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color getColor();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceFeature[] getSequenceFeatures();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param v DOCUMENT ME!
+     */
+    public void setSequenceFeatures(SequenceFeature [] features);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id DOCUMENT ME!
+     */
+    public void setPDBId(Vector ids);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getPDBId();
+
+    public void addPDBId(PDBEntry entry);
+
+    public String getVamsasId();
+
+    public void setVamsasId(String id);
+
+    public void setDBRef(DBRefEntry[] dbs);
+
+    public DBRefEntry [] getDBRef();
+
+    public void addDBRef(DBRefEntry entry);
+
+    public void addSequenceFeature(SequenceFeature sf);
+
+    public void setDatasetSequence(SequenceI seq);
+
+    public SequenceI getDatasetSequence();
+
+    public AlignmentAnnotation [] getAnnotation();
+
+    public void addAlignmentAnnotation(AlignmentAnnotation annotation);
+
+    public SequenceGroup getHiddenSequences();
+
+    public void addHiddenSequence(SequenceI seq);
+
+    public void showHiddenSequence(SequenceI seq);
+
+    public void changeCase(boolean toUpper, int start, int end);
+
+    public void toggleCase(int start, int end);
+
+  /**
+   * getSubSequence from start to end of sequence
+   * @param start first residue in subSequence
+   * @return SequenceI
+   */
+  public SequenceI getSubSequence(int start);
+  /**
+   * remove all gaps in the sequence
+   * @return number of gaps removed
+   */
+  public int removeGaps();
+  /**
+   * remove all gaps from start to end columns in sequence
+   * @param start 
+   * @param end
+   * @return number of gaps removed
+   */
+  public int removeGaps(int start, int end);
+
+}