-package jalview.analysis;\r
-\r
-import java.util.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class Finder\r
-{\r
- /**\r
- * Implements the search algorithms for the Find dialog box.\r
- */\r
- SearchResults searchResults;\r
- AlignmentI alignment;\r
- jalview.datamodel.SequenceGroup selection = null;\r
- Vector idMatch = null;\r
- boolean caseSensitive = false;\r
- boolean findAll = false;\r
- com.stevesoft.pat.Regex regex = null;\r
- /**\r
- * hold's last-searched position between calles to find(false)\r
- */\r
- int seqIndex = 0, resIndex = 0;\r
- public Finder(AlignmentI alignment, SequenceGroup selection)\r
- {\r
- this.alignment = alignment;\r
- this.selection = selection;\r
- }\r
-\r
- public Finder(AlignmentI alignment, SequenceGroup selectionGroup,\r
- int seqIndex, int resIndex)\r
- {\r
- this(alignment, selectionGroup);\r
- this.seqIndex = seqIndex;\r
- this.resIndex = resIndex;\r
- }\r
-\r
- public boolean find(String searchString)\r
- {\r
- boolean hasResults = false;\r
- if (!caseSensitive)\r
- {\r
- searchString = searchString.toUpperCase();\r
- }\r
- regex = new com.stevesoft.pat.Regex(searchString);\r
- searchResults = new SearchResults();\r
- idMatch = new Vector();\r
- Sequence seq;\r
- String item = null;\r
- boolean found = false;\r
-\r
- ////// is the searchString a residue number?\r
- try\r
- {\r
- int res = Integer.parseInt(searchString);\r
- found = true;\r
- if (selection == null || selection.getSize() < 1)\r
- {\r
- seq = (Sequence) alignment.getSequenceAt(0);\r
- }\r
- else\r
- {\r
- seq = (Sequence) (selection.getSequenceAt(0));\r
- }\r
-\r
- searchResults.addResult(seq, res, res);\r
- hasResults = true;\r
- }\r
- catch (NumberFormatException ex)\r
- {\r
- }\r
-\r
- ///////////////////////////////////////////////\r
-\r
- int end = alignment.getHeight();\r
-\r
- if (selection != null)\r
- {\r
- if ( (selection.getSize() < 1) ||\r
- ( (selection.getEndRes() - selection.getStartRes()) < 2))\r
- {\r
- selection = null;\r
- }\r
- }\r
-\r
- while (!found && (seqIndex < end))\r
- {\r
- seq = (Sequence) alignment.getSequenceAt(seqIndex);\r
-\r
- if ( (selection != null) && !selection.getSequences(null).contains(seq))\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
-\r
- continue;\r
- }\r
-\r
- item = seq.getSequenceAsString();\r
- // JBPNote - check if this toUpper which is present in the application implementation makes a difference\r
- //if(!caseSensitive)\r
- // item = item.toUpperCase();\r
-\r
- if ( (selection != null) &&\r
- (selection.getEndRes() < alignment.getWidth() - 1))\r
- {\r
- item = item.substring(0, selection.getEndRes() + 1);\r
- }\r
-\r
- ///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not\r
- StringBuffer noGapsSB = new StringBuffer();\r
- int insertCount = 0;\r
- Vector spaces = new Vector();\r
-\r
- for (int j = 0; j < item.length(); j++)\r
- {\r
- if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
- {\r
- noGapsSB.append(item.charAt(j));\r
- spaces.addElement(new Integer(insertCount));\r
- }\r
- else\r
- {\r
- insertCount++;\r
- }\r
- }\r
-\r
- String noGaps = noGapsSB.toString();\r
-\r
- for (int r = resIndex; r < noGaps.length(); r++)\r
- {\r
-\r
- if (regex.searchFrom(noGaps, r))\r
- {\r
- resIndex = regex.matchedFrom();\r
-\r
- if ( (selection != null) &&\r
- ( (resIndex +\r
- Integer.parseInt(spaces.elementAt(resIndex).toString())) <\r
- selection.getStartRes()))\r
- {\r
- continue;\r
- }\r
-\r
- int sres = seq.findPosition(resIndex +\r
- Integer.parseInt(spaces.elementAt(\r
- resIndex)\r
- .toString()));\r
- int eres = seq.findPosition(regex.matchedTo() - 1 +\r
- Integer.parseInt(spaces.elementAt(regex.\r
- matchedTo() -\r
- 1).toString()));\r
-\r
- searchResults.addResult(seq, sres, eres);\r
- hasResults = true;\r
- if (!findAll)\r
- {\r
- // thats enough, break and display the result\r
- found = true;\r
- resIndex++;\r
-\r
- break;\r
- }\r
-\r
- r = resIndex;\r
- }\r
- else\r
- {\r
- break;\r
- }\r
- }\r
-\r
- if (!found)\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
- }\r
- }\r
-\r
- for (int id = 0; id < alignment.getHeight(); id++)\r
- {\r
- if (regex.search(alignment.getSequenceAt(id).getName()))\r
- {\r
- idMatch.addElement(alignment.getSequenceAt(id));\r
- hasResults = true;\r
- }\r
- }\r
- return hasResults;\r
- }\r
-\r
- /**\r
- * @return the alignment\r
- */\r
- public AlignmentI getAlignment()\r
- {\r
- return alignment;\r
- }\r
-\r
- /**\r
- * @param alignment the alignment to set\r
- */\r
- public void setAlignment(AlignmentI alignment)\r
- {\r
- this.alignment = alignment;\r
- }\r
-\r
- /**\r
- * @return the caseSensitive\r
- */\r
- public boolean isCaseSensitive()\r
- {\r
- return caseSensitive;\r
- }\r
-\r
- /**\r
- * @param caseSensitive the caseSensitive to set\r
- */\r
- public void setCaseSensitive(boolean caseSensitive)\r
- {\r
- this.caseSensitive = caseSensitive;\r
- }\r
-\r
- /**\r
- * @return the findAll\r
- */\r
- public boolean isFindAll()\r
- {\r
- return findAll;\r
- }\r
-\r
- /**\r
- * @param findAll the findAll to set\r
- */\r
- public void setFindAll(boolean findAll)\r
- {\r
- this.findAll = findAll;\r
- }\r
-\r
- /**\r
- * @return the selection\r
- */\r
- public jalview.datamodel.SequenceGroup getSelection()\r
- {\r
- return selection;\r
- }\r
-\r
- /**\r
- * @param selection the selection to set\r
- */\r
- public void setSelection(jalview.datamodel.SequenceGroup selection)\r
- {\r
- this.selection = selection;\r
- }\r
-\r
- /**\r
- * @return the idMatch\r
- */\r
- public Vector getIdMatch()\r
- {\r
- return idMatch;\r
- }\r
-\r
- /**\r
- * @return the regex\r
- */\r
- public com.stevesoft.pat.Regex getRegex()\r
- {\r
- return regex;\r
- }\r
-\r
- /**\r
- * @return the searchResults\r
- */\r
- public SearchResults getSearchResults()\r
- {\r
- return searchResults;\r
- }\r
-\r
- /**\r
- * @return the resIndex\r
- */\r
- public int getResIndex()\r
- {\r
- return resIndex;\r
- }\r
-\r
- /**\r
- * @param resIndex the resIndex to set\r
- */\r
- public void setResIndex(int resIndex)\r
- {\r
- this.resIndex = resIndex;\r
- }\r
-\r
- /**\r
- * @return the seqIndex\r
- */\r
- public int getSeqIndex()\r
- {\r
- return seqIndex;\r
- }\r
-\r
- /**\r
- * @param seqIndex the seqIndex to set\r
- */\r
- public void setSeqIndex(int seqIndex)\r
- {\r
- this.seqIndex = seqIndex;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.analysis;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+
+import java.util.Vector;
+
+public class Finder
+{
+ /**
+ * Implements the search algorithms for the Find dialog box.
+ */
+ SearchResults searchResults;
+
+ AlignmentI alignment;
+
+ jalview.datamodel.SequenceGroup selection = null;
+
+ Vector idMatch = null;
+
+ boolean caseSensitive = false;
+
+ private boolean includeDescription = false;
+
+ boolean findAll = false;
+
+ com.stevesoft.pat.Regex regex = null;
+
+ /**
+ * hold's last-searched position between calles to find(false)
+ */
+ int seqIndex = 0, resIndex = -1;
+
+ public Finder(AlignmentI alignment, SequenceGroup selection)
+ {
+ this.alignment = alignment;
+ this.selection = selection;
+ }
+
+ /**
+ * restart search at given sequence and residue on alignment and (optionally)
+ * contained in selection
+ *
+ * @param alignment
+ * @param selectionGroup
+ * @param seqIndex
+ * @param resIndex
+ */
+ public Finder(AlignmentI alignment, SequenceGroup selectionGroup,
+ int seqIndex, int resIndex)
+ {
+ this(alignment, selectionGroup);
+ this.seqIndex = seqIndex;
+ this.resIndex = resIndex;
+ }
+
+ public boolean find(String searchString)
+ {
+ boolean hasResults = false;
+ if (!caseSensitive)
+ {
+ searchString = searchString.toUpperCase();
+ }
+ regex = new com.stevesoft.pat.Regex(searchString);
+ regex.setIgnoreCase(!caseSensitive);
+ searchResults = new SearchResults();
+ idMatch = new Vector();
+ Sequence seq;
+ String item = null;
+ boolean found = false;
+ int end = alignment.getHeight();
+
+ // /////////////////////////////////////////////
+
+ if (selection != null)
+ {
+ if ((selection.getSize() < 1)
+ || ((selection.getEndRes() - selection.getStartRes()) < 2))
+ {
+ selection = null;
+ }
+ }
+
+ while (!found && (seqIndex < end))
+ {
+ seq = (Sequence) alignment.getSequenceAt(seqIndex);
+
+ if ((selection != null && selection.getSize() > 0)
+ && !selection.getSequences(null).contains(seq))
+ {
+ seqIndex++;
+ resIndex = -1;
+
+ continue;
+ }
+ if (resIndex < 0)
+ {
+ resIndex = 0;
+ // test for one off matches - sequence position and sequence ID
+ // //// is the searchString a residue number?
+ try
+ {
+ int res = Integer.parseInt(searchString);
+ // possibly a residue number - check if valid for seq
+ if (seq.getEnd() >= res)
+ {
+ searchResults.addResult(seq, res, res);
+ hasResults = true;
+ // resIndex=seq.getLength();
+ // seqIndex++;
+ if (!findAll)
+ {
+ found = true;
+ break;
+ }
+ }
+ } catch (NumberFormatException ex)
+ {
+ }
+
+ if (regex.search(seq.getName()))
+ {
+ idMatch.addElement(seq);
+ hasResults = true;
+ if (!findAll)
+ {
+ // stop and return the match
+ found = true;
+ break;
+ }
+ }
+
+ if (isIncludeDescription() && seq.getDescription() != null
+ && regex.search(seq.getDescription()))
+ {
+ idMatch.addElement(seq);
+ hasResults = true;
+ if (!findAll)
+ {
+ // stop and return the match
+ found = true;
+ break;
+ }
+ }
+ }
+ item = seq.getSequenceAsString();
+
+ if ((selection != null)
+ && (selection.getEndRes() < alignment.getWidth() - 1))
+ {
+ item = item.substring(0, selection.getEndRes() + 1);
+ }
+
+ // /Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
+ StringBuffer noGapsSB = new StringBuffer();
+ int insertCount = 0;
+ Vector spaces = new Vector();
+
+ for (int j = 0; j < item.length(); j++)
+ {
+ if (!jalview.util.Comparison.isGap(item.charAt(j)))
+ {
+ noGapsSB.append(item.charAt(j));
+ spaces.addElement(new Integer(insertCount));
+ }
+ else
+ {
+ insertCount++;
+ }
+ }
+
+ String noGaps = noGapsSB.toString();
+
+ for (int r = resIndex; r < noGaps.length(); r++)
+ {
+
+ if (regex.searchFrom(noGaps, r))
+ {
+ resIndex = regex.matchedFrom();
+
+ if ((selection != null && selection.getSize() > 0)
+ && ((resIndex + Integer.parseInt(spaces.elementAt(
+ resIndex).toString())) < selection.getStartRes()))
+ {
+ continue;
+ }
+ // if invalid string used, then regex has no matched to/from
+ int sres = seq
+ .findPosition(resIndex
+ + Integer.parseInt(spaces.elementAt(resIndex)
+ .toString()));
+ int eres = seq.findPosition(regex.matchedTo()
+ - 1
+ + Integer.parseInt(spaces
+ .elementAt(regex.matchedTo() - 1).toString()));
+
+ searchResults.addResult(seq, sres, eres);
+ hasResults = true;
+ if (!findAll)
+ {
+ // thats enough, break and display the result
+ found = true;
+ resIndex++;
+
+ break;
+ }
+
+ r = resIndex;
+ }
+ else
+ {
+ break;
+ }
+ }
+
+ if (!found)
+ {
+ seqIndex++;
+ resIndex = -1;
+ }
+ }
+
+ /**
+ * We now search the Id string in the main search loop. for (int id = 0; id
+ * < alignment.getHeight(); id++) { if
+ * (regex.search(alignment.getSequenceAt(id).getName())) {
+ * idMatch.addElement(alignment.getSequenceAt(id)); hasResults = true; } }
+ */
+ return hasResults;
+ }
+
+ /**
+ * @return the alignment
+ */
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ /**
+ * @param alignment
+ * the alignment to set
+ */
+ public void setAlignment(AlignmentI alignment)
+ {
+ this.alignment = alignment;
+ }
+
+ /**
+ * @return the caseSensitive
+ */
+ public boolean isCaseSensitive()
+ {
+ return caseSensitive;
+ }
+
+ /**
+ * @param caseSensitive
+ * the caseSensitive to set
+ */
+ public void setCaseSensitive(boolean caseSensitive)
+ {
+ this.caseSensitive = caseSensitive;
+ }
+
+ /**
+ * @return the findAll
+ */
+ public boolean isFindAll()
+ {
+ return findAll;
+ }
+
+ /**
+ * @param findAll
+ * the findAll to set
+ */
+ public void setFindAll(boolean findAll)
+ {
+ this.findAll = findAll;
+ }
+
+ /**
+ * @return the selection
+ */
+ public jalview.datamodel.SequenceGroup getSelection()
+ {
+ return selection;
+ }
+
+ /**
+ * @param selection
+ * the selection to set
+ */
+ public void setSelection(jalview.datamodel.SequenceGroup selection)
+ {
+ this.selection = selection;
+ }
+
+ /**
+ * @return the idMatch
+ */
+ public Vector getIdMatch()
+ {
+ return idMatch;
+ }
+
+ /**
+ * @return the regex
+ */
+ public com.stevesoft.pat.Regex getRegex()
+ {
+ return regex;
+ }
+
+ /**
+ * @return the searchResults
+ */
+ public SearchResults getSearchResults()
+ {
+ return searchResults;
+ }
+
+ /**
+ * @return the resIndex
+ */
+ public int getResIndex()
+ {
+ return resIndex;
+ }
+
+ /**
+ * @param resIndex
+ * the resIndex to set
+ */
+ public void setResIndex(int resIndex)
+ {
+ this.resIndex = resIndex;
+ }
+
+ /**
+ * @return the seqIndex
+ */
+ public int getSeqIndex()
+ {
+ return seqIndex;
+ }
+
+ /**
+ * @param seqIndex
+ * the seqIndex to set
+ */
+ public void setSeqIndex(int seqIndex)
+ {
+ this.seqIndex = seqIndex;
+ }
+
+ public boolean isIncludeDescription()
+ {
+ return includeDescription;
+ }
+
+ public void setIncludeDescription(boolean includeDescription)
+ {
+ this.includeDescription = includeDescription;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff