*/\r
package jalview.datamodel;\r
\r
-import MCview.*;\r
-\r
-import jalview.analysis.*;\r
-\r
import java.awt.*;\r
\r
import java.util.*;\r
\r
\r
-public class Sequence implements SequenceI {\r
- protected String name;\r
- protected String sequence;\r
- protected String description;\r
- protected int start;\r
- protected int end;\r
- protected String displayId;\r
- protected Color color = Color.white;\r
- String pdbId;\r
- public Vector sequenceFeatures = new Vector();\r
-\r
- public Sequence(String name, String sequence, int start, int end) {\r
- this.name = name;\r
- this.sequence = sequence;\r
- this.start = start;\r
- this.end = end;\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class Sequence implements SequenceI\r
+{\r
+ SequenceI datasetSequence;\r
+ String name;\r
+ String sequence;\r
+ String description;\r
+ int start;\r
+ int end;\r
+ Color color = Color.white;\r
+ Vector pdbIds;\r
+ String vamsasId;\r
+ Vector dbrefs;\r
+\r
+ /** This annotation is displayed below the alignment but the\r
+ * positions are tied to the residues of this sequence */\r
+ Vector annotation;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public SequenceFeature [] sequenceFeatures;\r
+\r
+ /** This array holds hidden sequences\r
+ * of which this sequence is the representitive member of a group\r
+ */\r
+ SequenceGroup hiddenSequences;\r
+\r
+ /**\r
+ * Creates a new Sequence object.\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ * @param sequence DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ public Sequence(String name, String sequence, int start, int end)\r
+ {\r
+ this.name = name;\r
+ this.sequence = sequence;\r
+ this.start = start;\r
+ this.end = end;\r
+\r
+ parseId();\r
+\r
+ checkValidRange();\r
+ }\r
+\r
+ com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(\r
+ "[/][0-9]{1,}[-][0-9]{1,}$");\r
+ com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(\r
+ "[0-9]{1,}$");\r
+\r
+ void parseId()\r
+ {\r
+ // Does sequence have the /start-end signiature?\r
+ if(limitrx.search(name))\r
+ {\r
+ name = limitrx.left();\r
+ endrx.search(limitrx.stringMatched());\r
+ setStart( Integer.parseInt( limitrx.stringMatched().substring(1,endrx.matchedFrom()-1 )));\r
+ setEnd( Integer.parseInt( endrx.stringMatched() ));\r
+ }\r
+ }\r
+\r
+ void checkValidRange()\r
+ {\r
+ if (end < 1)\r
+ {\r
+ int endRes = 0;\r
+ char ch;\r
+ for (int j = 0; j < sequence.length(); j++)\r
+ {\r
+ ch = sequence.charAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ endRes++;\r
+ }\r
+ }\r
+ if (endRes > 0)\r
+ {\r
+ endRes += start - 1;\r
+ }\r
+\r
+ this.end = endRes;\r
+ }\r
\r
- setDisplayId();\r
}\r
\r
- public Sequence(String name, String sequence) {\r
- this(name, sequence, 1, sequence.length());\r
+ /**\r
+ * Creates a new Sequence object.\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ * @param sequence DOCUMENT ME!\r
+ */\r
+ public Sequence(String name, String sequence)\r
+ {\r
+ this(name, sequence, 1, -1);\r
}\r
\r
- public Sequence(SequenceI seq) {\r
+ /**\r
+ * Creates a new Sequence object.\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ public Sequence(SequenceI seq)\r
+ {\r
this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());\r
}\r
\r
- public void setSequenceFeatures(Vector v) {\r
- sequenceFeatures = v;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param v DOCUMENT ME!\r
+ */\r
+ public void setSequenceFeatures(SequenceFeature [] features)\r
+ {\r
+ sequenceFeatures = features;\r
}\r
\r
- public Vector getSequenceFeatures() {\r
+ public void addSequenceFeature(SequenceFeature sf)\r
+ {\r
+ if(sequenceFeatures==null)\r
+ {\r
+ sequenceFeatures = new SequenceFeature[0];\r
+ }\r
+\r
+ for(int i=0; i<sequenceFeatures.length; i++)\r
+ {\r
+ if(sequenceFeatures[i].equals(sf))\r
+ {\r
+ return;\r
+ }\r
+ }\r
+\r
+ SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];\r
+ System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);\r
+ temp[sequenceFeatures.length] = sf;\r
+\r
+\r
+ sequenceFeatures = temp;\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceFeature [] getSequenceFeatures()\r
+ {\r
return sequenceFeatures;\r
}\r
\r
- public void setPDBId(String id) {\r
- pdbId = id;\r
+ public void addPDBId(PDBEntry entry)\r
+ {\r
+ if(pdbIds == null)\r
+ pdbIds = new Vector();\r
+\r
+ pdbIds.addElement(entry);\r
}\r
\r
- public String getPDBId() {\r
- return pdbId;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param id DOCUMENT ME!\r
+ */\r
+ public void setPDBId(Vector id)\r
+ {\r
+ pdbIds = id;\r
}\r
\r
- public String getDisplayId() {\r
- return displayId;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getPDBId()\r
+ {\r
+ return pdbIds;\r
}\r
\r
- public void setDisplayId() {\r
- displayId = name + "/" + start + "-" + end;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDisplayId(boolean jvsuffix)\r
+ {\r
+ StringBuffer result = new StringBuffer(name);\r
+ if (jvsuffix)\r
+ {\r
+ result.append("/" + start + "-" + end);\r
+ }\r
+\r
+ return result.toString();\r
}\r
\r
- public void setName(String name) {\r
- this.name = name;\r
- setDisplayId();\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ */\r
+ public void setName(String name)\r
+ {\r
+ this.name = name;\r
+ this.parseId();\r
}\r
\r
- public String getName() {\r
- return this.name;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName()\r
+ {\r
+ return this.name;\r
}\r
\r
- public void setStart(int start) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param start DOCUMENT ME!\r
+ */\r
+ public void setStart(int start)\r
+ {\r
this.start = start;\r
- setDisplayId();\r
}\r
\r
- public int getStart() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getStart()\r
+ {\r
return this.start;\r
}\r
\r
- public void setEnd(int end) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ public void setEnd(int end)\r
+ {\r
this.end = end;\r
- setDisplayId();\r
}\r
\r
- public int getEnd() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getEnd()\r
+ {\r
return this.end;\r
}\r
\r
- public int getLength() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getLength()\r
+ {\r
return this.sequence.length();\r
}\r
\r
- public void setSequence(String seq) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ public void setSequence(String seq)\r
+ {\r
this.sequence = seq;\r
+ checkValidRange();\r
}\r
\r
- public String getSequence() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getSequence()\r
+ {\r
return this.sequence;\r
}\r
\r
- public String getSequence(int start, int end) {\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
// JBPNote - left to user to pad the result here (TODO:Decide on this policy)\r
- if (start >= sequence.length()) {\r
+ if (start >= sequence.length())\r
+ {\r
return "";\r
}\r
\r
- if (end >= sequence.length()) {\r
+ if (end >= sequence.length())\r
+ {\r
end = sequence.length();\r
}\r
\r
return this.sequence.substring(start, end);\r
}\r
\r
- public char getCharAt(int i) {\r
- if (i < sequence.length()) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public char getCharAt(int i)\r
+ {\r
+ if (i < sequence.length())\r
+ {\r
return sequence.charAt(i);\r
- } else {\r
+ }\r
+ else\r
+ {\r
return ' ';\r
}\r
}\r
\r
- public void setDescription(String desc) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param desc DOCUMENT ME!\r
+ */\r
+ public void setDescription(String desc)\r
+ {\r
this.description = desc;\r
}\r
\r
- public String getDescription() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDescription()\r
+ {\r
return this.description;\r
}\r
\r
- public int findIndex(int pos) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pos DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int findIndex(int pos)\r
+ {\r
// returns the alignment position for a residue\r
int j = start;\r
int i = 0;\r
\r
- while ((i < sequence.length()) && (j <= end) && (j <= pos)) {\r
- char c = sequence.charAt(i);\r
-\r
- if (!jalview.util.Comparison.isGap((c))) {\r
+ while ((i < sequence.length()) && (j <= end) && (j <= pos))\r
+ {\r
+ if (!jalview.util.Comparison.isGap(sequence.charAt(i)))\r
+ {\r
j++;\r
}\r
\r
i++;\r
}\r
\r
- if ((j == end) && (j < pos)) {\r
+ if ((j == end) && (j < pos))\r
+ {\r
return end + 1;\r
- } else {\r
+ }\r
+ else\r
+ {\r
return i;\r
}\r
}\r
\r
- public int findPosition(int i) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int findPosition(int i)\r
+ {\r
// Returns the sequence position for an alignment position\r
int j = 0;\r
int pos = start;\r
\r
- while ((j < i) && (j < sequence.length())) {\r
- char c = sequence.charAt(j);\r
-\r
- if (!jalview.util.Comparison.isGap((c))) {\r
+ while ((j < i) && (j < sequence.length()))\r
+ {\r
+ if (!jalview.util.Comparison.isGap((sequence.charAt(j))))\r
+ {\r
pos++;\r
}\r
\r
return pos;\r
}\r
\r
- public int[] gapMap() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int[] gapMap()\r
+ {\r
// Returns an int array giving the position of each residue in the sequence in the alignment\r
String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);\r
int[] map = new int[seq.length()];\r
int j = 0;\r
int p = 0;\r
\r
- while (j < sequence.length()) {\r
- if (!jalview.util.Comparison.isGap(sequence.charAt(j))) {\r
+ while (j < sequence.length())\r
+ {\r
+ if (!jalview.util.Comparison.isGap(sequence.charAt(j)))\r
+ {\r
map[p++] = j;\r
}\r
\r
return map;\r
}\r
\r
- public void deleteCharAt(int i) {\r
- if (i >= sequence.length()) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ */\r
+ public void deleteCharAt(int i)\r
+ {\r
+ if (i >= sequence.length())\r
+ {\r
return;\r
}\r
\r
sequence = sequence.substring(0, i) + sequence.substring(i + 1);\r
}\r
\r
- public void deleteChars(int i, int j) {\r
- if (i >= sequence.length()) {\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
+ if (i >= sequence.length())\r
+ {\r
return;\r
}\r
\r
- if (j >= sequence.length()) {\r
+ if (j >= sequence.length())\r
+ {\r
sequence = sequence.substring(0, i);\r
- } else {\r
+ }\r
+ else\r
+ {\r
sequence = sequence.substring(0, i) + sequence.substring(j);\r
}\r
}\r
\r
- public void insertCharAt(int i, char c) {\r
- insertCharAt(i, c, true);\r
- }\r
\r
- public void insertCharAt(int i, char c, boolean chop) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param c DOCUMENT ME!\r
+ * @param chop DOCUMENT ME!\r
+ */\r
+ public void insertCharAt(int i, char c)\r
+ {\r
String tmp = new String(sequence);\r
\r
- if (i < sequence.length()) {\r
+ if (i < sequence.length())\r
+ {\r
sequence = tmp.substring(0, i) + String.valueOf(c) +\r
tmp.substring(i);\r
- } else {\r
+ }\r
+ else\r
+ {\r
// JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!\r
char[] ch = new char[(1 + i) - sequence.length()];\r
\r
}\r
}\r
\r
- public void setColor(Color c) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ */\r
+ public void setColor(Color c)\r
+ {\r
this.color = c;\r
}\r
\r
- public Color getColor() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Color getColor()\r
+ {\r
return color;\r
}\r
+\r
+ public String getVamsasId()\r
+ {\r
+ return vamsasId;\r
+ }\r
+\r
+ public void setVamsasId(String id)\r
+ {\r
+ vamsasId = id;\r
+ }\r
+\r
+ public void setDBRef(Vector dbref)\r
+ {\r
+ dbrefs = dbref;\r
+ }\r
+ public Vector getDBRef()\r
+ {\r
+ return dbrefs;\r
+ }\r
+\r
+ public void addDBRef(DBRefEntry entry)\r
+ {\r
+ if(dbrefs == null)\r
+ dbrefs = new Vector();\r
+\r
+ dbrefs.addElement(entry);\r
+ }\r
+\r
+ public void setDatasetSequence(SequenceI seq)\r
+ {\r
+ datasetSequence = seq;\r
+ }\r
+\r
+ public SequenceI getDatasetSequence()\r
+ {\r
+ return datasetSequence;\r
+ }\r
+\r
+ public AlignmentAnnotation [] getAnnotation()\r
+ {\r
+ if(annotation==null)\r
+ return null;\r
+\r
+ AlignmentAnnotation [] ret = new AlignmentAnnotation[annotation.size()];\r
+ for(int r = 0; r<ret.length; r++)\r
+ ret[r] = (AlignmentAnnotation)annotation.elementAt(r);\r
+\r
+ return ret;\r
+ }\r
+\r
+ public void addAlignmentAnnotation(AlignmentAnnotation annotation)\r
+ {\r
+ if(this.annotation==null)\r
+ this.annotation = new Vector();\r
+\r
+ this.annotation.addElement( annotation );\r
+ }\r
+\r
+ public SequenceGroup getHiddenSequences()\r
+ {\r
+ return hiddenSequences;\r
+ }\r
+\r
+ public void addHiddenSequence(SequenceI seq)\r
+ {\r
+ if(hiddenSequences==null)\r
+ {\r
+ hiddenSequences = new SequenceGroup();\r
+ }\r
+ hiddenSequences.addSequence(seq, false);\r
+ }\r
+\r
+ public void showHiddenSequence(SequenceI seq)\r
+ {\r
+ hiddenSequences.deleteSequence(seq, false);\r
+ if (hiddenSequences.getSize() < 1)\r
+ {\r
+ hiddenSequences = null;\r
+ }\r
+\r
+ }\r
+\r
+ public void changeCase(boolean toUpper, int start, int end)\r
+ {\r
+ StringBuffer newSeq = new StringBuffer();\r
+\r
+ if(end>sequence.length())\r
+ end = sequence.length();\r
+\r
+ if (start > 0)\r
+ {\r
+ newSeq.append(sequence.substring(0, start));\r
+ }\r
+\r
+ if (toUpper)\r
+ newSeq.append(sequence.substring(start, end).toUpperCase());\r
+ else\r
+ newSeq.append(sequence.substring(start, end).toLowerCase());\r
+\r
+ if (end < sequence.length())\r
+ newSeq.append(sequence.substring(end));\r
+\r
+ sequence = newSeq.toString();\r
+ }\r
+\r
+ public void toggleCase(int start, int end)\r
+ {\r
+ StringBuffer newSeq = new StringBuffer();\r
+\r
+ if(end>sequence.length())\r
+ end = sequence.length();\r
+\r
+ if (start > 0)\r
+ {\r
+ newSeq.append(sequence.substring(0, start));\r
+ }\r
+\r
+ char nextChar;\r
+ for(int c=start; c<end; c++)\r
+ {\r
+ nextChar = sequence.charAt(c);\r
+ if(Character.isLetter(nextChar))\r
+ {\r
+ if(Character.isUpperCase(nextChar))\r
+ nextChar = Character.toLowerCase(nextChar);\r
+ else\r
+ nextChar = Character.toUpperCase(nextChar);\r
+ }\r
+\r
+\r
+ newSeq.append(nextChar);\r
+ }\r
+\r
+ if (end < sequence.length())\r
+ newSeq.append(sequence.substring(end));\r
+\r
+ sequence = newSeq.toString();\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff