From: jprocter <Jim Procter>
Date: Wed, 31 Oct 2007 17:42:12 +0000 (+0000)
Subject: javadoc
X-Git-Tag: Release_2_4~205
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=69cc05ae896ee0c80b55571919dec8a4ba31de6c;p=jalview.git

javadoc
---

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 0514fb8..21dcce1 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,278 +1,281 @@
-/*
- * 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;
-
-import java.util.*;
-
-public class HiddenSequences
-{
-  public SequenceI[] hiddenSequences;
-  AlignmentI alignment;
-
-  public HiddenSequences(AlignmentI al)
-  {
-    alignment = al;
-  }
-
-  public int getSize()
-  {
-    if (hiddenSequences == null)
-    {
-      return 0;
-    }
-    int count = 0;
-    for (int i = 0; i < hiddenSequences.length; i++)
-    {
-      if (hiddenSequences[i] != null)
-      {
-        count++;
-      }
-    }
-
-    return count;
-  }
-
-  public int getWidth()
-  {
-    int width = 0;
-    for (int i = 0; i < hiddenSequences.length; i++)
-    {
-      if (hiddenSequences[i] != null && hiddenSequences[i].getLength() > width)
-      {
-        width = hiddenSequences[i].getLength();
-      }
-    }
-
-    return width;
-  }
-
-  /**
-   * Call this method if sequences are removed from the
-   * main alignment
-   */
-  public void adjustHeightSequenceDeleted(int seqIndex)
-  {
-    if (hiddenSequences == null)
-    {
-      return;
-    }
-
-    int alHeight = alignment.getHeight();
-
-    SequenceI[] tmp = new SequenceI[alHeight + getSize()];
-    int deletionIndex = adjustForHiddenSeqs(seqIndex);
-
-    for (int i = 0; i < hiddenSequences.length; i++)
-    {
-      if (hiddenSequences[i] == null)
-      {
-        continue;
-      }
-
-      if (i > deletionIndex)
-      {
-        tmp[i - 1] = hiddenSequences[i];
-      }
-      else
-      {
-        tmp[i] = hiddenSequences[i];
-      }
-    }
-
-    hiddenSequences = tmp;
-
-  }
-
-  /**
-   * Call this method if sequences are added to or removed from the
-   * main alignment
-   */
-  public void adjustHeightSequenceAdded()
-  {
-    if (hiddenSequences == null)
-    {
-      return;
-    }
-
-    int alHeight = alignment.getHeight();
-
-    SequenceI[] tmp = new SequenceI[alHeight + getSize()];
-    System.arraycopy(hiddenSequences, 0, tmp, 0, hiddenSequences.length);
-    hiddenSequences = tmp;
-  }
-
-  public void hideSequence(SequenceI sequence)
-  {
-    if (hiddenSequences == null)
-    {
-      hiddenSequences = new SequenceI[alignment.getHeight()];
-    }
-
-    int alignmentIndex = alignment.findIndex(sequence);
-    alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
-
-    if (hiddenSequences[alignmentIndex] != null)
-    {
-      System.out.println("ERROR!!!!!!!!!!!");
-    }
-
-    hiddenSequences[alignmentIndex] = sequence;
-
-    alignment.deleteSequence(sequence);
-  }
-
-  public Vector showAll(Hashtable hiddenReps)
-  {
-    Vector revealedSeqs = new Vector();
-    for (int i = 0; i < hiddenSequences.length; i++)
-    {
-      if (hiddenSequences[i] != null)
-      {
-        Vector tmp = showSequence(i, hiddenReps);
-        for (int t = 0; t < tmp.size(); t++)
-        {
-          revealedSeqs.addElement(tmp.elementAt(t));
-        }
-      }
-    }
-    return revealedSeqs;
-  }
-
-  public Vector showSequence(int alignmentIndex, Hashtable hiddenReps)
-  {
-    Vector revealedSeqs = new Vector();
-    SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
-    if (repSequence != null &&
-        hiddenReps != null
-        && hiddenReps.containsKey(repSequence))
-    {
-      hiddenReps.remove(repSequence);
-      revealedSeqs.addElement(repSequence);
-    }
-
-    int start = adjustForHiddenSeqs(alignmentIndex - 1);
-    int end = adjustForHiddenSeqs(alignmentIndex);
-    if (end >= hiddenSequences.length)
-    {
-      end = hiddenSequences.length - 1;
-    }
-
-    for (int index = end; index > start; index--)
-    {
-      SequenceI seq = hiddenSequences[index];
-      hiddenSequences[index] = null;
-
-      if (seq != null)
-      {
-        if (seq.getLength() > 0)
-        {
-          revealedSeqs.addElement(seq);
-          alignment.getSequences().insertElementAt(seq, alignmentIndex);
-        }
-        else
-        {
-          System.out.println(seq.getName() + " has been deleted whilst hidden");
-        }
-      }
-
-    }
-
-    return revealedSeqs;
-  }
-
-  public SequenceI getHiddenSequence(int alignmentIndex)
-  {
-    return hiddenSequences[alignmentIndex];
-  }
-
-  public int findIndexWithoutHiddenSeqs(int alignmentIndex)
-  {
-    int index = 0;
-    int hiddenSeqs = 0;
-    if (hiddenSequences.length <= alignmentIndex)
-    {
-      alignmentIndex = hiddenSequences.length - 1;
-    }
-
-    while (index <= alignmentIndex)
-    {
-      if (hiddenSequences[index] != null)
-      {
-        hiddenSeqs++;
-      }
-      index++;
-    }
-    ;
-
-    return (alignmentIndex - hiddenSeqs);
-  }
-
-  public int adjustForHiddenSeqs(int alignmentIndex)
-  {
-    int index = 0;
-    int hSize = hiddenSequences.length;
-    while (index <= alignmentIndex && index < hSize)
-    {
-      if (hiddenSequences[index] != null)
-      {
-        alignmentIndex++;
-      }
-      index++;
-    }
-    ;
-
-    return alignmentIndex;
-  }
-
-  public AlignmentI getFullAlignment()
-  {
-    int isize = hiddenSequences.length;
-    SequenceI[] seq = new Sequence[isize];
-
-    int index = 0;
-    for (int i = 0; i < hiddenSequences.length; i++)
-    {
-      if (hiddenSequences[i] != null)
-      {
-        seq[i] = hiddenSequences[i];
-      }
-      else
-      {
-        seq[i] = alignment.getSequenceAt(index);
-        index++;
-      }
-    }
-
-    return new Alignment(seq);
-  }
-
-  public boolean isHidden(SequenceI seq)
-  {
-    for (int i = 0; i < hiddenSequences.length; i++)
-    {
-      if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
-      {
-        return true;
-      }
-    }
-
-    return false;
-  }
-}
+/*
+ * 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;
+
+import java.util.*;
+
+public class HiddenSequences
+{
+  /**
+   * holds a list of hidden sequences associated with an alignment.
+   */
+  public SequenceI[] hiddenSequences;
+  AlignmentI alignment;
+
+  public HiddenSequences(AlignmentI al)
+  {
+    alignment = al;
+  }
+
+  public int getSize()
+  {
+    if (hiddenSequences == null)
+    {
+      return 0;
+    }
+    int count = 0;
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null)
+      {
+        count++;
+      }
+    }
+
+    return count;
+  }
+
+  public int getWidth()
+  {
+    int width = 0;
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null && hiddenSequences[i].getLength() > width)
+      {
+        width = hiddenSequences[i].getLength();
+      }
+    }
+
+    return width;
+  }
+
+  /**
+   * Call this method if sequences are removed from the
+   * main alignment
+   */
+  public void adjustHeightSequenceDeleted(int seqIndex)
+  {
+    if (hiddenSequences == null)
+    {
+      return;
+    }
+
+    int alHeight = alignment.getHeight();
+
+    SequenceI[] tmp = new SequenceI[alHeight + getSize()];
+    int deletionIndex = adjustForHiddenSeqs(seqIndex);
+
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] == null)
+      {
+        continue;
+      }
+
+      if (i > deletionIndex)
+      {
+        tmp[i - 1] = hiddenSequences[i];
+      }
+      else
+      {
+        tmp[i] = hiddenSequences[i];
+      }
+    }
+
+    hiddenSequences = tmp;
+
+  }
+
+  /**
+   * Call this method if sequences are added to or removed from the
+   * main alignment
+   */
+  public void adjustHeightSequenceAdded()
+  {
+    if (hiddenSequences == null)
+    {
+      return;
+    }
+
+    int alHeight = alignment.getHeight();
+
+    SequenceI[] tmp = new SequenceI[alHeight + getSize()];
+    System.arraycopy(hiddenSequences, 0, tmp, 0, hiddenSequences.length);
+    hiddenSequences = tmp;
+  }
+
+  public void hideSequence(SequenceI sequence)
+  {
+    if (hiddenSequences == null)
+    {
+      hiddenSequences = new SequenceI[alignment.getHeight()];
+    }
+
+    int alignmentIndex = alignment.findIndex(sequence);
+    alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
+
+    if (hiddenSequences[alignmentIndex] != null)
+    {
+      System.out.println("ERROR!!!!!!!!!!!");
+    }
+
+    hiddenSequences[alignmentIndex] = sequence;
+
+    alignment.deleteSequence(sequence);
+  }
+
+  public Vector showAll(Hashtable hiddenReps)
+  {
+    Vector revealedSeqs = new Vector();
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null)
+      {
+        Vector tmp = showSequence(i, hiddenReps);
+        for (int t = 0; t < tmp.size(); t++)
+        {
+          revealedSeqs.addElement(tmp.elementAt(t));
+        }
+      }
+    }
+    return revealedSeqs;
+  }
+
+  public Vector showSequence(int alignmentIndex, Hashtable hiddenReps)
+  {
+    Vector revealedSeqs = new Vector();
+    SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
+    if (repSequence != null &&
+        hiddenReps != null
+        && hiddenReps.containsKey(repSequence))
+    {
+      hiddenReps.remove(repSequence);
+      revealedSeqs.addElement(repSequence);
+    }
+
+    int start = adjustForHiddenSeqs(alignmentIndex - 1);
+    int end = adjustForHiddenSeqs(alignmentIndex);
+    if (end >= hiddenSequences.length)
+    {
+      end = hiddenSequences.length - 1;
+    }
+
+    for (int index = end; index > start; index--)
+    {
+      SequenceI seq = hiddenSequences[index];
+      hiddenSequences[index] = null;
+
+      if (seq != null)
+      {
+        if (seq.getLength() > 0)
+        {
+          revealedSeqs.addElement(seq);
+          alignment.getSequences().insertElementAt(seq, alignmentIndex);
+        }
+        else
+        {
+          System.out.println(seq.getName() + " has been deleted whilst hidden");
+        }
+      }
+
+    }
+
+    return revealedSeqs;
+  }
+
+  public SequenceI getHiddenSequence(int alignmentIndex)
+  {
+    return hiddenSequences[alignmentIndex];
+  }
+
+  public int findIndexWithoutHiddenSeqs(int alignmentIndex)
+  {
+    int index = 0;
+    int hiddenSeqs = 0;
+    if (hiddenSequences.length <= alignmentIndex)
+    {
+      alignmentIndex = hiddenSequences.length - 1;
+    }
+
+    while (index <= alignmentIndex)
+    {
+      if (hiddenSequences[index] != null)
+      {
+        hiddenSeqs++;
+      }
+      index++;
+    }
+    ;
+
+    return (alignmentIndex - hiddenSeqs);
+  }
+
+  public int adjustForHiddenSeqs(int alignmentIndex)
+  {
+    int index = 0;
+    int hSize = hiddenSequences.length;
+    while (index <= alignmentIndex && index < hSize)
+    {
+      if (hiddenSequences[index] != null)
+      {
+        alignmentIndex++;
+      }
+      index++;
+    }
+    ;
+
+    return alignmentIndex;
+  }
+
+  public AlignmentI getFullAlignment()
+  {
+    int isize = hiddenSequences.length;
+    SequenceI[] seq = new Sequence[isize];
+
+    int index = 0;
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null)
+      {
+        seq[i] = hiddenSequences[i];
+      }
+      else
+      {
+        seq[i] = alignment.getSequenceAt(index);
+        index++;
+      }
+    }
+
+    return new Alignment(seq);
+  }
+
+  public boolean isHidden(SequenceI seq)
+  {
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+      {
+        return true;
+      }
+    }
+
+    return false;
+  }
+}