X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=34c1cd917f6f0fb252de743de48435710db7bfae;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=3853af9891fcd5efd390bdc95438ffe97d9d3f8f;hpb=9257b8510c7354cbd7e43a3fc2817978cc8e4ae9;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 3853af9..34c1cd9 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -27,7 +27,14 @@ import java.awt.*;
 import java.util.*;
 
 
-public class Sequence implements SequenceI {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Sequence implements SequenceI
+{
     protected String name;
     protected String sequence;
     protected String description;
@@ -36,9 +43,20 @@ public class Sequence implements SequenceI {
     protected String displayId;
     protected Color color = Color.white;
     String pdbId;
+
+    /** DOCUMENT ME!! */
     public Vector sequenceFeatures = new Vector();
 
-    public Sequence(String name, String sequence, int start, int end) {
+    /**
+     * Creates a new Sequence object.
+     *
+     * @param name DOCUMENT ME!
+     * @param sequence DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public Sequence(String name, String sequence, int start, int end)
+    {
         this.name = name;
         this.sequence = sequence;
         this.start = start;
@@ -47,137 +65,295 @@ public class Sequence implements SequenceI {
         setDisplayId();
     }
 
-    public Sequence(String name, String sequence) {
+    /**
+     * Creates a new Sequence object.
+     *
+     * @param name DOCUMENT ME!
+     * @param sequence DOCUMENT ME!
+     */
+    public Sequence(String name, String sequence)
+    {
         this(name, sequence, 1, sequence.length());
     }
 
-    public Sequence(SequenceI seq) {
+    /**
+     * Creates a new Sequence object.
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public Sequence(SequenceI seq)
+    {
         this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
     }
 
-    public void setSequenceFeatures(Vector v) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param v DOCUMENT ME!
+     */
+    public void setSequenceFeatures(Vector v)
+    {
         sequenceFeatures = v;
     }
 
-    public Vector getSequenceFeatures() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getSequenceFeatures()
+    {
         return sequenceFeatures;
     }
 
-    public void setPDBId(String id) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id DOCUMENT ME!
+     */
+    public void setPDBId(String id)
+    {
         pdbId = id;
     }
 
-    public String getPDBId() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getPDBId()
+    {
         return pdbId;
     }
 
-    public String getDisplayId() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDisplayId()
+    {
         return displayId;
     }
 
-    public void setDisplayId() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void setDisplayId()
+    {
         displayId = name + "/" + start + "-" + end;
     }
 
-    public void setName(String name) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
         this.name = name;
         setDisplayId();
     }
 
-    public String getName() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
+    {
         return this.name;
     }
 
-    public void setStart(int start) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     */
+    public void setStart(int start)
+    {
         this.start = start;
         setDisplayId();
     }
 
-    public int getStart() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStart()
+    {
         return this.start;
     }
 
-    public void setEnd(int end) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param end DOCUMENT ME!
+     */
+    public void setEnd(int end)
+    {
         this.end = end;
         setDisplayId();
     }
 
-    public int getEnd() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEnd()
+    {
         return this.end;
     }
 
-    public int getLength() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getLength()
+    {
         return this.sequence.length();
     }
 
-    public void setSequence(String seq) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void setSequence(String seq)
+    {
         this.sequence = seq;
     }
 
-    public String getSequence() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getSequence()
+    {
         return this.sequence;
     }
 
-    public String getSequence(int start, int end) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getSequence(int start, int end)
+    {
         // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
-        if (start >= sequence.length()) {
+        if (start >= sequence.length())
+        {
             return "";
         }
 
-        if (end >= sequence.length()) {
+        if (end >= sequence.length())
+        {
             end = sequence.length();
         }
 
         return this.sequence.substring(start, end);
     }
 
-    public char getCharAt(int i) {
-        if (i < sequence.length()) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char getCharAt(int i)
+    {
+        if (i < sequence.length())
+        {
             return sequence.charAt(i);
-        } else {
+        }
+        else
+        {
             return ' ';
         }
     }
 
-    public void setDescription(String desc) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param desc DOCUMENT ME!
+     */
+    public void setDescription(String desc)
+    {
         this.description = desc;
     }
 
-    public String getDescription() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDescription()
+    {
         return this.description;
     }
 
-    public int findIndex(int pos) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pos DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int findIndex(int pos)
+    {
         // returns the alignment position for a residue
         int j = start;
         int i = 0;
 
-        while ((i < sequence.length()) && (j <= end) && (j <= pos)) {
+        while ((i < sequence.length()) && (j <= end) && (j <= pos))
+        {
             char c = sequence.charAt(i);
 
-            if (!jalview.util.Comparison.isGap((c))) {
+            if (!jalview.util.Comparison.isGap((c)))
+            {
                 j++;
             }
 
             i++;
         }
 
-        if ((j == end) && (j < pos)) {
+        if ((j == end) && (j < pos))
+        {
             return end + 1;
-        } else {
+        }
+        else
+        {
             return i;
         }
     }
 
-    public int findPosition(int i) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int findPosition(int i)
+    {
         // Returns the sequence position for an alignment position
         int j = 0;
         int pos = start;
 
-        while ((j < i) && (j < sequence.length())) {
+        while ((j < i) && (j < sequence.length()))
+        {
             char c = sequence.charAt(j);
 
-            if (!jalview.util.Comparison.isGap((c))) {
+            if (!jalview.util.Comparison.isGap((c)))
+            {
                 pos++;
             }
 
@@ -187,15 +363,23 @@ public class Sequence implements SequenceI {
         return pos;
     }
 
-    public int[] gapMap() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int[] gapMap()
+    {
         // Returns an int array giving the position of each residue in the sequence in the alignment
         String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);
         int[] map = new int[seq.length()];
         int j = 0;
         int p = 0;
 
-        while (j < sequence.length()) {
-            if (!jalview.util.Comparison.isGap(sequence.charAt(j))) {
+        while (j < sequence.length())
+        {
+            if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
+            {
                 map[p++] = j;
             }
 
@@ -205,37 +389,73 @@ public class Sequence implements SequenceI {
         return map;
     }
 
-    public void deleteCharAt(int i) {
-        if (i >= sequence.length()) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void deleteCharAt(int i)
+    {
+        if (i >= sequence.length())
+        {
             return;
         }
 
         sequence = sequence.substring(0, i) + sequence.substring(i + 1);
     }
 
-    public void deleteChars(int i, int j) {
-        if (i >= sequence.length()) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     */
+    public void deleteChars(int i, int j)
+    {
+        if (i >= sequence.length())
+        {
             return;
         }
 
-        if (j >= sequence.length()) {
+        if (j >= sequence.length())
+        {
             sequence = sequence.substring(0, i);
-        } else {
+        }
+        else
+        {
             sequence = sequence.substring(0, i) + sequence.substring(j);
         }
     }
 
-    public void insertCharAt(int i, char c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     */
+    public void insertCharAt(int i, char c)
+    {
         insertCharAt(i, c, true);
     }
 
-    public void insertCharAt(int i, char c, boolean chop) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     * @param chop DOCUMENT ME!
+     */
+    public void insertCharAt(int i, char c, boolean chop)
+    {
         String tmp = new String(sequence);
 
-        if (i < sequence.length()) {
+        if (i < sequence.length())
+        {
             sequence = tmp.substring(0, i) + String.valueOf(c) +
                 tmp.substring(i);
-        } else {
+        }
+        else
+        {
             // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!
             char[] ch = new char[(1 + i) - sequence.length()];
 
@@ -246,11 +466,23 @@ public class Sequence implements SequenceI {
         }
     }
 
-    public void setColor(Color c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setColor(Color c)
+    {
         this.color = c;
     }
 
-    public Color getColor() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color getColor()
+    {
         return color;
     }
 }