-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-public class SearchResults\r
-{\r
-\r
- Match[] matches;\r
-\r
- /**\r
- * This method replaces the old search results which merely\r
- * held an alignment index of search matches. This broke\r
- * when sequences were moved around the alignment\r
- * @param seq Sequence\r
- * @param start int\r
- * @param end int\r
- */\r
- public void addResult(SequenceI seq, int start, int end)\r
- {\r
- if (matches == null)\r
- {\r
- matches = new Match[]\r
- {\r
- new Match(seq, start, end)};\r
- return;\r
- }\r
-\r
- int mSize = matches.length;\r
-\r
- Match[] tmp = new Match[mSize + 1];\r
- int m;\r
- for (m = 0; m < mSize; m++)\r
- {\r
- tmp[m] = matches[m];\r
- }\r
-\r
- tmp[m] = new Match(seq, start, end);\r
-\r
- matches = tmp;\r
- }\r
-\r
- /**\r
- * This Method returns the search matches which lie between the\r
- * start and end points of the sequence in question. It is\r
- * optimised for returning objects for drawing on SequenceCanvas\r
- */\r
- public int[] getResults(SequenceI sequence, int start, int end)\r
- {\r
- if (matches == null)\r
- {\r
- return null;\r
- }\r
-\r
- int[] result = null;\r
- int[] tmp = null;\r
- int resultLength;\r
-\r
- for (int m = 0; m < matches.length; m++)\r
- {\r
- if (matches[m].sequence == sequence)\r
- {\r
- int matchStart = matches[m].sequence.findIndex(matches[m].start) - 1;\r
- int matchEnd = matches[m].sequence.findIndex(matches[m].end) - 1;\r
-\r
- if (matchStart <= end && matchEnd >= start)\r
- {\r
- if (matchStart < start)\r
- {\r
- matchStart = start;\r
- }\r
-\r
- if (matchEnd > end)\r
- {\r
- matchEnd = end;\r
- }\r
-\r
- if (result == null)\r
- {\r
- result = new int[]\r
- {\r
- matchStart, matchEnd};\r
- }\r
- else\r
- {\r
- resultLength = result.length;\r
- tmp = new int[resultLength + 2];\r
- System.arraycopy(result, 0, tmp, 0, resultLength);\r
- result = tmp;\r
- result[resultLength] = matchStart;\r
- result[resultLength + 1] = matchEnd;\r
- }\r
- }\r
- }\r
- }\r
- return result;\r
- }\r
-\r
- public int getSize()\r
- {\r
- return matches == null ? 0 : matches.length;\r
- }\r
-\r
- public SequenceI getResultSequence(int index)\r
- {\r
- return matches[index].sequence;\r
- }\r
-\r
- public int getResultStart(int index)\r
- {\r
- return matches[index].start;\r
- }\r
-\r
- public int getResultEnd(int index)\r
- {\r
- return matches[index].end;\r
- }\r
-\r
- class Match\r
- {\r
- SequenceI sequence;\r
- int start;\r
- int end;\r
-\r
- public Match(SequenceI seq, int start, int end)\r
- {\r
- sequence = seq;\r
- this.start = start;\r
- this.end = end;\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+public class SearchResults
+{
+
+ Match[] matches;
+
+ /**
+ * This method replaces the old search results which merely held an alignment
+ * index of search matches. This broke when sequences were moved around the
+ * alignment
+ *
+ * @param seq
+ * Sequence
+ * @param start
+ * int
+ * @param end
+ * int
+ */
+ public void addResult(SequenceI seq, int start, int end)
+ {
+ if (matches == null)
+ {
+ matches = new Match[]
+ { new Match(seq, start, end) };
+ return;
+ }
+
+ int mSize = matches.length;
+
+ Match[] tmp = new Match[mSize + 1];
+ int m;
+ for (m = 0; m < mSize; m++)
+ {
+ tmp[m] = matches[m];
+ }
+
+ tmp[m] = new Match(seq, start, end);
+
+ matches = tmp;
+ }
+
+ /**
+ * Quickly check if the given sequence is referred to in the search results
+ *
+ * @param sequence
+ * (specific alignment sequence or a dataset sequence)
+ * @return true if the results involve sequence
+ */
+ public boolean involvesSequence(SequenceI sequence)
+ {
+ if (matches == null || matches.length == 0)
+ {
+ return false;
+ }
+ SequenceI ds = sequence.getDatasetSequence();
+ for (int m = 0; m < matches.length; m++)
+ {
+ if (matches[m].sequence != null
+ && (matches[m].sequence == sequence || matches[m].sequence == ds))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * This Method returns the search matches which lie between the start and end
+ * points of the sequence in question. It is optimised for returning objects
+ * for drawing on SequenceCanvas
+ */
+ public int[] getResults(SequenceI sequence, int start, int end)
+ {
+ if (matches == null)
+ {
+ return null;
+ }
+
+ int[] result = null;
+ int[] tmp = null;
+ int resultLength, matchStart = 0, matchEnd = 0;
+ boolean mfound;
+ for (int m = 0; m < matches.length; m++)
+ {
+ mfound = false;
+ if (matches[m].sequence == sequence)
+ {
+ mfound = true;
+ // locate aligned position
+ matchStart = sequence.findIndex(matches[m].start) - 1;
+ matchEnd = sequence.findIndex(matches[m].end) - 1;
+ }
+ else if (matches[m].sequence == sequence.getDatasetSequence())
+ {
+ mfound = true;
+ // locate region in local context
+ matchStart = sequence.findIndex(matches[m].start) - 1;
+ matchEnd = sequence.findIndex(matches[m].end) - 1;
+ }
+ if (mfound)
+ {
+ if (matchStart <= end && matchEnd >= start)
+ {
+ if (matchStart < start)
+ {
+ matchStart = start;
+ }
+
+ if (matchEnd > end)
+ {
+ matchEnd = end;
+ }
+
+ if (result == null)
+ {
+ result = new int[]
+ { matchStart, matchEnd };
+ }
+ else
+ {
+ resultLength = result.length;
+ tmp = new int[resultLength + 2];
+ System.arraycopy(result, 0, tmp, 0, resultLength);
+ result = tmp;
+ result[resultLength] = matchStart;
+ result[resultLength + 1] = matchEnd;
+ }
+ }
+ else
+ {
+ // debug
+ // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
+ // + matchEnd+"<"+start);
+ }
+ }
+ }
+ return result;
+ }
+
+ public int getSize()
+ {
+ return matches == null ? 0 : matches.length;
+ }
+
+ public SequenceI getResultSequence(int index)
+ {
+ return matches[index].sequence;
+ }
+
+ public int getResultStart(int index)
+ {
+ return matches[index].start;
+ }
+
+ public int getResultEnd(int index)
+ {
+ return matches[index].end;
+ }
+
+ class Match
+ {
+ SequenceI sequence;
+
+ int start;
+
+ int end;
+
+ public Match(SequenceI seq, int start, int end)
+ {
+ sequence = seq;
+ this.start = start;
+ this.end = end;
+ }
+ }
+}