X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=6de42b9d23e704384ecc0af78a279b1bab9765a7;hb=cb8ec179c020265666678572815ab056a024da22;hp=0ae9ec2bb1e2702d88b639ecba6615c142b66740;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 0ae9ec2..6de42b9 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,49 +1,62 @@
 /*
-* 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
-*/
+ * 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 jalview.analysis.*;
 
-import jalview.datamodel.*;
-
 import jalview.schemes.*;
 
 import java.awt.*;
 
-import java.util.Vector;
+import java.util.*;
 
 
-public class SequenceGroup {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceGroup
+{
     String groupName;
     Conservation conserve;
     Vector aaFrequency;
     boolean displayBoxes;
     boolean displayText;
     boolean colourText;
+
+    /** DOCUMENT ME!! */
     public Vector sequences = new Vector();
     int width = -1;
+
+    /** DOCUMENT ME!! */
     public ColourSchemeI cs;
     int startRes = 0;
     int endRes = 0;
     Color outlineColour = Color.black;
 
-    public SequenceGroup() {
+    /**
+     * Creates a new SequenceGroup object.
+     */
+    public SequenceGroup()
+    {
         groupName = "Group";
         this.displayBoxes = true;
         this.displayText = true;
@@ -51,9 +64,48 @@ public class SequenceGroup {
         cs = null;
     }
 
+    /**
+     * Creates a new SequenceGroup object.
+     *
+     * @param sequences DOCUMENT ME!
+     * @param groupName DOCUMENT ME!
+     * @param scheme DOCUMENT ME!
+     * @param displayBoxes DOCUMENT ME!
+     * @param displayText DOCUMENT ME!
+     * @param colourText DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public SequenceGroup(Vector sequences, String groupName,
+        ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
+        boolean colourText, int start, int end)
+    {
+        this.sequences = sequences;
+        this.groupName = groupName;
+        this.displayBoxes = displayBoxes;
+        this.displayText = displayText;
+        this.colourText = colourText;
+        this.cs = scheme;
+        startRes = start;
+        endRes = end;
+        recalcConservation();
+    }
+
+    /**
+     * Creates a new SequenceGroup object.
+     *
+     * @param groupName DOCUMENT ME!
+     * @param scheme DOCUMENT ME!
+     * @param displayBoxes DOCUMENT ME!
+     * @param displayText DOCUMENT ME!
+     * @param colourText DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
     public SequenceGroup(String groupName, ColourSchemeI scheme,
         boolean displayBoxes, boolean displayText, boolean colourText,
-        int start, int end) {
+        int start, int end)
+    {
         this.groupName = groupName;
         this.displayBoxes = displayBoxes;
         this.displayText = displayText;
@@ -63,19 +115,32 @@ public class SequenceGroup {
         endRes = end;
     }
 
-    public boolean adjustForRemoveLeft(int col) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean adjustForRemoveLeft(int col)
+    {
         // return value is true if the group still exists
-        if (startRes >= col) {
+        if (startRes >= col)
+        {
             startRes = startRes - col;
         }
 
-        if (endRes >= col) {
+        if (endRes >= col)
+        {
             endRes = endRes - col;
 
-            if (startRes > endRes) {
+            if (startRes > endRes)
+            {
                 startRes = 0;
             }
-        } else {
+        }
+        else
+        {
             // must delete this group!!
             return false;
         }
@@ -83,137 +148,298 @@ public class SequenceGroup {
         return true;
     }
 
-    public boolean adjustForRemoveRight(int col) {
-        if (startRes > col) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean adjustForRemoveRight(int col)
+    {
+        if (startRes > col)
+        {
             // delete this group
             return false;
         }
 
-        if (endRes >= col) {
+        if (endRes >= col)
+        {
             endRes = col;
         }
 
         return true;
     }
 
-    public String getName() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
+    {
         return groupName;
     }
 
-    public void setName(String name) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
         groupName = name;
     }
 
-    public Conservation getConservation() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Conservation getConservation()
+    {
         return conserve;
     }
 
-    public void setConservation(Conservation c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setConservation(Conservation c)
+    {
         conserve = c;
     }
 
-    public void addSequence(SequenceI s) {
-        if (!sequences.contains(s)) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param recalc DOCUMENT ME!
+     */
+    public void addSequence(SequenceI s, boolean recalc)
+    {
+        if (!sequences.contains(s))
+        {
             sequences.addElement(s);
         }
 
-        if (cs != null) {
-            cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
-        }
-
-        if (cs instanceof ConservationColourScheme) {
+        if (recalc)
+        {
             recalcConservation();
         }
     }
 
-    void recalcConservation() {
-        Conservation c = new Conservation(groupName,
-                ResidueProperties.propHash, 3, sequences, 0, getWidth());
-        c.calculate();
-        c.verdict(false, 25);
+    /**
+     * DOCUMENT ME!
+     */
+    public void recalcConservation()
+    {
+        if(cs == null)
+          return;
+
+        cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+
+
+        if (cs instanceof ClustalxColourScheme)
+        {
+            ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+        }
+
+
+        if (cs.conservationApplied())
+        {
+            Conservation c = new Conservation(groupName,
+                    ResidueProperties.propHash, 3, sequences, 0, getWidth());
+            c.calculate();
+            c.verdict(false, 25);
+
 
-        ConservationColourScheme ccs = (ConservationColourScheme) cs;
-        ccs.conserve = c;
+            cs.setConservation(c);
+
+            if (cs instanceof ClustalxColourScheme)
+            {
+                ((ClustalxColourScheme) cs).resetClustalX(sequences,
+                    getWidth());
+            }
+        }
     }
 
-    public void addOrRemove(SequenceI s) {
-        if (sequences.contains(s)) {
-            deleteSequence(s);
-        } else {
-            addSequence(s);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param recalc DOCUMENT ME!
+     */
+    public void addOrRemove(SequenceI s, boolean recalc)
+    {
+        if (sequences.contains(s))
+        {
+            deleteSequence(s, recalc);
+        }
+        else
+        {
+            addSequence(s, recalc);
         }
     }
 
-    public void deleteSequence(SequenceI s) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param recalc DOCUMENT ME!
+     */
+    public void deleteSequence(SequenceI s, boolean recalc)
+    {
         sequences.removeElement(s);
 
-        if (cs != null) {
-            cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
-        }
-
-        if (cs instanceof ConservationColourScheme) {
+        if (recalc)
+        {
             recalcConservation();
         }
     }
 
-    public int getStartRes() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartRes()
+    {
         return startRes;
     }
 
-    public int getEndRes() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEndRes()
+    {
         return endRes;
     }
 
-    public void setStartRes(int i) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void setStartRes(int i)
+    {
         startRes = i;
     }
 
-    public void setEndRes(int i) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void setEndRes(int i)
+    {
         endRes = i;
     }
 
-    public int getSize() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSize()
+    {
         return sequences.size();
     }
 
-    public SequenceI getSequenceAt(int i) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI getSequenceAt(int i)
+    {
         return (SequenceI) sequences.elementAt(i);
     }
 
-    public void setColourText(boolean state) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setColourText(boolean state)
+    {
         colourText = state;
     }
 
-    public boolean getColourText() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getColourText()
+    {
         return colourText;
     }
 
-    public void setDisplayText(boolean state) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setDisplayText(boolean state)
+    {
         displayText = state;
     }
 
-    public boolean getDisplayText() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getDisplayText()
+    {
         return displayText;
     }
 
-    public void setDisplayBoxes(boolean state) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setDisplayBoxes(boolean state)
+    {
         displayBoxes = state;
     }
 
-    public boolean getDisplayBoxes() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getDisplayBoxes()
+    {
         return displayBoxes;
     }
 
-    public int getWidth() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getWidth()
+    {
         // MC This needs to get reset when characters are inserted and deleted
-        if (sequences.size() > 0) {
+        if (sequences.size() > 0)
+        {
             width = ((SequenceI) sequences.elementAt(0)).getLength();
         }
 
-        for (int i = 1; i < sequences.size(); i++) {
+        for (int i = 1; i < sequences.size(); i++)
+        {
             SequenceI seq = (SequenceI) sequences.elementAt(i);
 
-            if (seq.getLength() > width) {
+            if (seq.getLength() > width)
+            {
                 width = seq.getLength();
             }
         }
@@ -221,11 +447,23 @@ public class SequenceGroup {
         return width;
     }
 
-    public void setOutlineColour(Color c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setOutlineColour(Color c)
+    {
         outlineColour = c;
     }
 
-    public Color getOutlineColour() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color getOutlineColour()
+    {
         return outlineColour;
     }
 
@@ -236,12 +474,14 @@ public class SequenceGroup {
      * @param al Alignment
      * @return SequenceI[]
      */
-    public SequenceI[] getSequencesInOrder(Alignment al) {
-        int sz;
+    public SequenceI[] getSequencesInOrder(AlignmentI al)
+    {
+        int sz = sequences.size();
         java.util.Hashtable orderedSeqs = new java.util.Hashtable();
-        SequenceI[] seqs = new SequenceI[sz = sequences.size()];
+        SequenceI[] seqs = new SequenceI[sz];
 
-        for (int i = 0; i < sz; i++) {
+        for (int i = 0; i < sz; i++)
+        {
             SequenceI seq = (SequenceI) sequences.elementAt(i);
             int index = al.findIndex(seq);
             orderedSeqs.put(index + "", seq);
@@ -249,21 +489,12 @@ public class SequenceGroup {
 
         int index = 0;
 
-        for (int i = 0; i < sz; i++) {
-            SequenceI seq = null;
-
-            while (seq == null) {
-                if (orderedSeqs.containsKey(index + "")) {
-                    seq = (SequenceI) orderedSeqs.get(index + "");
-                    index++;
-
-                    break;
-                } else {
-                    index++;
-                }
+        for (int i = 0; i < al.getHeight(); i++)
+        {
+            if (orderedSeqs.containsKey(i + ""))
+            {
+                seqs[index++] = (SequenceI) orderedSeqs.get(i + "");
             }
-
-            seqs[index] = seq;
         }
 
         return seqs;