*/\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
+/**\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 shortName;\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
+\r
+ /** DOCUMENT ME!! */\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
+ * 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
+ parseId();\r
+\r
+ this.sequence = sequence;\r
+ this.start = start;\r
+ this.end = end;\r
+\r
+ checkValidRange();\r
+ }\r
+\r
+ void parseId()\r
+ {\r
+ // Read in any DB refs first\r
+ StringTokenizer st = new StringTokenizer(name, "|");\r
+ if(st.countTokens()<1)\r
+ {\r
+ shortName = name;\r
+ return;\r
+ }\r
+\r
+ while (st.countTokens() > 1)\r
+ {\r
+ String a = st.nextToken();\r
+ String b = st.nextToken();\r
+ addDBRef(new DBRefEntry(a, "0", b));\r
+ }\r
+\r
+ if (st.hasMoreTokens())\r
+ shortName = st.nextToken();\r
+\r
+ // Remove /start-end from sequence\r
+ if (shortName.indexOf("/") > 0)\r
+ {\r
+ st = new StringTokenizer(shortName, "/");\r
+ String limits = null;\r
+ try\r
+ {\r
+ if (st.countTokens() == 2)\r
+ {\r
+\r
+ shortName = st.nextToken();\r
+\r
+ limits = st.nextToken();\r
+\r
+ st = new StringTokenizer(limits, "-");\r
+\r
+ if (st.countTokens() == 2)\r
+ {\r
+ setStart(Integer.valueOf(st.nextToken()).intValue());\r
+ setEnd(Integer.valueOf(st.nextToken()).intValue());\r
+ }\r
+ }\r
+\r
+ // If we're still in this loop, parsing of start and end was ok\r
+ // Therefore remove it from the sequence name\r
+ name = name.substring(0, name.indexOf("/"));\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {\r
+ // Problem parsing sequence limits. Just add it back to the\r
+ // Id so we dont lose this info\r
+ shortName += "/" + limits;\r
+ }\r
+ }\r
\r
- setDisplayId();\r
}\r
\r
- public Sequence(String name, String sequence) {\r
- this(name, sequence, 1, sequence.length());\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
}\r
\r
- public Sequence(SequenceI seq) {\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
+ /**\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param v DOCUMENT ME!\r
+ */\r
+ public void setSequenceFeatures(Vector v)\r
+ {\r
sequenceFeatures = v;\r
}\r
\r
- public Vector getSequenceFeatures() {\r
- return sequenceFeatures;\r
+ public void addSequenceFeature(SequenceFeature sf)\r
+ {\r
+ if(sequenceFeatures==null)\r
+ sequenceFeatures = new Vector();\r
+\r
+ sequenceFeatures.addElement(sf);\r
}\r
\r
- public void setPDBId(String id) {\r
- pdbId = id;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getSequenceFeatures()\r
+ {\r
+ return sequenceFeatures;\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 dbref, boolean jvsuffix)\r
+ {\r
+ StringBuffer result = new StringBuffer();\r
+ if (dbref && dbrefs != null)\r
+ {\r
+ for (int i = 0; i < dbrefs.size(); i++)\r
+ {\r
+ DBRefEntry entry = (DBRefEntry) dbrefs.elementAt(i);\r
+ result.append(entry.getSource() + "|" + entry.getAccessionId() + "|");\r
+ }\r
+ }\r
+\r
+ result.append(shortName);\r
+\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
+ while ((i < sequence.length()) && (j <= end) && (j <= pos))\r
+ {\r
char c = sequence.charAt(i);\r
\r
- if (!jalview.util.Comparison.isGap((c))) {\r
+ if (!jalview.util.Comparison.isGap((c)))\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
+ while ((j < i) && (j < sequence.length()))\r
+ {\r
char c = sequence.charAt(j);\r
\r
- if (!jalview.util.Comparison.isGap((c))) {\r
+ if (!jalview.util.Comparison.isGap((c)))\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param c DOCUMENT ME!\r
+ */\r
+ public void insertCharAt(int i, char c)\r
+ {\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, boolean chop)\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
}\r
git://source.jalview.org / jalview.git / blobdiff