- j++;\r
- }\r
- return map;\r
- }\r
-\r
- public void deleteCharAt(int i)\r
- {\r
- if (i>=sequence.length())\r
- return;\r
- sequence = sequence.substring(0,i) + sequence.substring(i+1);\r
- }\r
-\r
- public void deleteChars(int i, int j)\r
- {\r
- if (i>=sequence.length())\r
- return;\r
- if (j>=sequence.length())\r
- sequence = sequence.substring(0,i);\r
- else\r
- sequence = sequence.substring(0,i) + sequence.substring(j);\r
- }\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
- String tmp = new String(sequence);\r
-\r
- if (i < sequence.length()) {\r
- sequence = tmp.substring(0,i) + String.valueOf(c) + tmp.substring(i);\r
- } else {\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
- for (int j=0, k=ch.length; j<k; j++)\r
- ch[j] = c;\r
- sequence = tmp + String.valueOf(ch);\r
- }\r
-\r
- }\r
-\r
- public void setColor(Color c) {\r
- this.color = c;\r
- }\r
-\r
- public Color getColor() {\r
- return color;\r
- }\r
+\r
+ return result.toString();\r
+ }\r
+\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName()\r
+ {\r
+ return this.name;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param start DOCUMENT ME!\r
+ */\r
+ public void setStart(int start)\r
+ {\r
+ this.start = start;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getStart()\r
+ {\r
+ return this.start;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ public void setEnd(int end)\r
+ {\r
+ this.end = end;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getEnd()\r
+ {\r
+ return this.end;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getLength()\r
+ {\r
+ return this.sequence.length();\r
+ }\r
+\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getSequence()\r
+ {\r
+ return this.sequence;\r
+ }\r
+\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
+ {\r
+ return "";\r
+ }\r
+\r
+ if (end >= sequence.length())\r
+ {\r
+ end = sequence.length();\r
+ }\r
+\r
+ return this.sequence.substring(start, end);\r
+ }\r
+\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
+ }\r
+ else\r
+ {\r
+ return ' ';\r
+ }\r
+ }\r
+\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDescription()\r
+ {\r
+ return this.description;\r
+ }\r
+\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
+ {\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
+ {\r
+ return end + 1;\r
+ }\r
+ else\r
+ {\r
+ return i;\r
+ }\r
+ }\r
+\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
+ {\r
+ if (!jalview.util.Comparison.isGap((sequence.charAt(j))))\r
+ {\r
+ pos++;\r
+ }\r
+\r
+ j++;\r
+ }\r
+\r
+ return pos;\r
+ }\r
+\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
+ {\r
+ if (!jalview.util.Comparison.isGap(sequence.charAt(j)))\r
+ {\r
+ map[p++] = j;\r
+ }\r
+\r
+ j++;\r
+ }\r
+\r
+ return map;\r
+ }\r
+\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
+ /**\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
+ {\r
+ sequence = sequence.substring(0, i);\r
+ }\r
+ else\r
+ {\r
+ sequence = sequence.substring(0, i) + sequence.substring(j);\r
+ }\r
+ }\r
+\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
+ /**\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
+ {\r
+ sequence = tmp.substring(0, i) + String.valueOf(c) +\r
+ tmp.substring(i);\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
+ for (int j = 0, k = ch.length; j < k; j++)\r
+ ch[j] = c;\r
+\r
+ sequence = tmp + String.valueOf(ch);\r
+ }\r
+ }\r
+\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
+ /**\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