X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=191f6e832ae0dd24176b8705d6c65dd09cec9283;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=2fa09aa730be1bcc7c89831f6712607b7ac9bded;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 2fa09aa..191f6e8 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,308 +1,398 @@
-package jalview.analysis;
-
-import java.util.*;
-
-import jalview.datamodel.*;
-
-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;
- boolean findAll = false;
- com.stevesoft.pat.Regex regex = null;
- /**
- * hold's last-searched position between calles to find(false)
- */
- int seqIndex = 0, resIndex = 0;
- public Finder(AlignmentI alignment, SequenceGroup selection)
- {
- this.alignment = alignment;
- this.selection = selection;
- }
-
- 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);
- searchResults = new SearchResults();
- idMatch = new Vector();
- Sequence seq;
- String item = null;
- boolean found = false;
-
- ////// is the searchString a residue number?
- try
- {
- int res = Integer.parseInt(searchString);
- found = true;
- if (selection == null || selection.getSize() < 1)
- {
- seq = (Sequence) alignment.getSequenceAt(0);
- }
- else
- {
- seq = (Sequence) (selection.getSequenceAt(0));
- }
-
- searchResults.addResult(seq, res, res);
- hasResults = true;
- }
- catch (NumberFormatException ex)
- {
- }
-
- ///////////////////////////////////////////////
-
- 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.getSequences(null).contains(seq))
- {
- seqIndex++;
- resIndex = 0;
-
- continue;
- }
-
- item = seq.getSequenceAsString();
- // JBPNote - check if this toUpper which is present in the application implementation makes a difference
- //if(!caseSensitive)
- // item = item.toUpperCase();
-
- 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) &&
- ( (resIndex +
- Integer.parseInt(spaces.elementAt(resIndex).toString())) <
- selection.getStartRes()))
- {
- continue;
- }
-
- 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 = 0;
- }
- }
-
- 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;
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
+import com.stevesoft.pat.Regex;
+
+public class Finder
+{
+ /**
+ * Implements the search algorithms for the Find dialog box.
+ */
+ SearchResultsI searchResults;
+
+ AlignmentI alignment;
+
+ SequenceGroup selection = null;
+
+ Vector idMatch = null;
+
+ boolean caseSensitive = false;
+
+ private boolean includeDescription = false;
+
+ boolean findAll = false;
+
+ Regex regex = null;
+
+ /**
+ * holds last-searched position between calls 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 Regex(searchString);
+ regex.setIgnoreCase(!caseSensitive);
+ searchResults = new SearchResults();
+ idMatch = new Vector();
+ String item = null;
+ boolean found = false;
+ int end = alignment.getHeight();
+
+ // /////////////////////////////////////////////
+
+ if (selection != null)
+ {
+ if ((selection.getSize() < 1)
+ || ((selection.getEndRes() - selection.getStartRes()) < 2))
+ {
+ selection = null;
+ }
+ }
+ SearchResultMatchI lastm = null;
+
+ while (!found && (seqIndex < end))
+ {
+ SequenceI seq = 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.contains(seq))
+ {
+ 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.contains(seq))
+ {
+ 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
+ StringBuilder noGapsSB = new StringBuilder();
+ int insertCount = 0;
+ List spaces = new ArrayList();
+
+ for (int j = 0; j < item.length(); j++)
+ {
+ if (!Comparison.isGap(item.charAt(j)))
+ {
+ noGapsSB.append(item.charAt(j));
+ spaces.add(Integer.valueOf(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
+ + spaces.get(resIndex) < selection.getStartRes()))
+ {
+ continue;
+ }
+ // if invalid string used, then regex has no matched to/from
+ int sres = seq.findPosition(resIndex + spaces.get(resIndex));
+ int eres = seq.findPosition(regex.matchedTo() - 1
+ + (spaces.get(regex.matchedTo() - 1)));
+ // only add result if not contained in previous result
+ if (lastm == null || (lastm.getSequence() != seq
+ || (!(lastm.getStart() <= sres
+ && lastm.getEnd() >= eres))))
+ {
+ lastm = 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;
+ }
+
+ /**
+ * Returns the (possibly empty) list of matching sequences (when search
+ * includes searching sequence names)
+ *
+ * @return
+ */
+ public Vector getIdMatch()
+ {
+ return idMatch;
+ }
+
+ /**
+ * @return the regex
+ */
+ public com.stevesoft.pat.Regex getRegex()
+ {
+ return regex;
+ }
+
+ /**
+ * @return the searchResults
+ */
+ public SearchResultsI 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;
+ }
+}