X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=a7fcb3310f19b66b7b2962b771260d7ddc8cb4b6;hb=54266d19e6e16f170d9994d6acee33313ab7b59a;hp=3853af9891fcd5efd390bdc95438ffe97d9d3f8f;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 3853af9..a7fcb33 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -18,166 +18,449 @@
 */
 package jalview.datamodel;
 
-import MCview.*;
-
-import jalview.analysis.*;
-
 import java.awt.*;
 
 import java.util.*;
 
 
-public class Sequence implements SequenceI {
-    protected String name;
-    protected String sequence;
-    protected String description;
-    protected int start;
-    protected int end;
-    protected String displayId;
-    protected Color color = Color.white;
-    String pdbId;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Sequence implements SequenceI
+{
+    SequenceI datasetSequence;
+    String name;
+    String shortName;
+    String sequence;
+    String description;
+    int start;
+    int end;
+    Color color = Color.white;
+    Vector pdbIds;
+    String vamsasId;
+    Vector dbrefs;
+
+
+    /** DOCUMENT ME!! */
     public Vector sequenceFeatures = new Vector();
 
-    public Sequence(String name, String sequence, int start, int end) {
-        this.name = name;
-        this.sequence = sequence;
-        this.start = start;
-        this.end = 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;
+      parseId();
+
+      this.sequence = sequence;
+      this.start = start;
+      this.end = end;
+
+      checkValidRange();
+    }
+
+    void parseId()
+    {
+        // Read in any DB refs first
+         StringTokenizer st = new StringTokenizer(name, "|");
+         if(st.countTokens()<1)
+         {
+           shortName = name;
+           return;
+         }
+
+         while (st.countTokens() > 1)
+         {
+           String a = st.nextToken();
+           String b = st.nextToken();
+           addDBRef(new DBRefEntry(a, "0", b));
+         }
+
+         if (st.hasMoreTokens())
+           shortName = st.nextToken();
+
+         // Remove /start-end from sequence
+         if (shortName.indexOf("/") > 0)
+         {
+           st = new StringTokenizer(shortName, "/");
+           String limits = null;
+           try
+           {
+             if (st.countTokens() == 2)
+             {
+
+               shortName = st.nextToken();
+
+               limits = st.nextToken();
+
+               st = new StringTokenizer(limits, "-");
+
+               if (st.countTokens() == 2)
+               {
+                 setStart(Integer.valueOf(st.nextToken()).intValue());
+                 setEnd(Integer.valueOf(st.nextToken()).intValue());
+               }
+             }
+
+             // If we're still in this loop, parsing of start and end was ok
+             // Therefore remove it from the sequence name
+             name = name.substring(0, name.indexOf("/"));
+           }
+           catch (NumberFormatException ex)
+           {
+             // Problem parsing sequence limits. Just add it back to the
+             // Id so we dont lose this info
+             shortName += "/" + limits;
+           }
+         }
 
-        setDisplayId();
     }
 
-    public Sequence(String name, String sequence) {
-        this(name, sequence, 1, sequence.length());
+    void checkValidRange()
+    {
+      if (end < 1)
+      {
+        int endRes = 0;
+        char ch;
+        for (int j = 0; j < sequence.length(); j++)
+        {
+          ch = sequence.charAt(j);
+          if (!jalview.util.Comparison.isGap( (ch)))
+          {
+            endRes++;
+          }
+        }
+        if (endRes > 0)
+        {
+          endRes += start - 1;
+        }
+
+        this.end = endRes;
+      }
+
     }
 
-    public Sequence(SequenceI seq) {
+    /**
+     * Creates a new Sequence object.
+     *
+     * @param name DOCUMENT ME!
+     * @param sequence DOCUMENT ME!
+     */
+    public Sequence(String name, String sequence)
+    {
+        this(name, sequence, 1, -1);
+    }
+
+    /**
+     * 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() {
+    public void addSequenceFeature(SequenceFeature sf)
+    {
+      if(sequenceFeatures==null)
+        sequenceFeatures = new Vector();
+
+      sequenceFeatures.addElement(sf);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getSequenceFeatures()
+    {
         return sequenceFeatures;
     }
 
-    public void setPDBId(String id) {
-        pdbId = id;
+    public void addPDBId(PDBEntry entry)
+    {
+      if(pdbIds == null)
+        pdbIds = new Vector();
+
+      pdbIds.addElement(entry);
     }
 
-    public String getPDBId() {
-        return pdbId;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id DOCUMENT ME!
+     */
+    public void setPDBId(Vector id)
+    {
+        pdbIds = id;
     }
 
-    public String getDisplayId() {
-        return displayId;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getPDBId()
+    {
+        return pdbIds;
     }
 
-    public void setDisplayId() {
-        displayId = name + "/" + start + "-" + end;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDisplayId(boolean dbref, boolean jvsuffix)
+    {
+      StringBuffer result = new StringBuffer();
+      if (dbref && dbrefs != null)
+      {
+        for (int i = 0; i < dbrefs.size(); i++)
+        {
+          DBRefEntry entry = (DBRefEntry) dbrefs.elementAt(i);
+          result.append(entry.getSource() + "|" + entry.getAccessionId() + "|");
+        }
+      }
+
+      result.append(shortName);
+
+      if (jvsuffix)
+      {
+        result.append("/" + start + "-" + end);
+      }
+
+      return result.toString();
     }
 
-    public void setName(String name) {
-        this.name = name;
-        setDisplayId();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
+      this.name = name;
+      this.parseId();
     }
 
-    public String getName() {
-        return this.name;
+    /**
+     * 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;
+        checkValidRange();
     }
 
-    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 +470,23 @@ 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 +496,73 @@ 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 +573,66 @@ 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;
     }
+
+    public String getVamsasId()
+    {
+      return vamsasId;
+    }
+
+    public void setVamsasId(String id)
+    {
+      vamsasId = id;
+    }
+
+    public void setDBRef(Vector dbref)
+    {
+      dbrefs = dbref;
+    }
+    public Vector getDBRef()
+    {
+      return dbrefs;
+    }
+
+    public void addDBRef(DBRefEntry entry)
+    {
+      if(dbrefs == null)
+        dbrefs = new Vector();
+
+      dbrefs.addElement(entry);
+    }
+
+    public void setDatasetSequence(SequenceI seq)
+    {
+      datasetSequence = seq;
+    }
+
+    public SequenceI getDatasetSequence()
+    {
+      return datasetSequence;
+    }
+
+    public String getShortName()
+    {
+      return shortName;
+    }
+
 }