-package jalview.analysis;
-import java.util.Vector;
-
-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.add(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.get(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.add(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;
- }
-}
+package jalview.analysis;\r
+import java.util.Vector;\r
+\r
+import jalview.datamodel.*;\r
+\r
+public class Finder {\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
+ this.alignment=alignment;\r
+ this.selection = selection;\r
+ }\r
+\r
+ public Finder(AlignmentI alignment, SequenceGroup selectionGroup, int seqIndex, int resIndex) {\r
+ this(alignment, selectionGroup);\r
+ this.seqIndex=seqIndex;\r
+ this.resIndex=resIndex;\r
+ }\r
+\r
+ public boolean find(String searchString) {\r
+ boolean hasResults=false;\r
+ if(!caseSensitive)\r
+ searchString = searchString.toUpperCase();\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
+\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())) < selection.getStartRes()))\r
+ {\r
+ continue;\r
+ }\r
+\r
+\r
+ int sres = seq.findPosition(resIndex +\r
+ Integer.parseInt(spaces.elementAt(resIndex)\r
+ .toString()));\r
+ int eres = seq.findPosition(regex.matchedTo() - 1 +\r
+ Integer.parseInt(spaces.elementAt(regex.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
+ * @return the alignment\r
+ */\r
+ public AlignmentI getAlignment() {\r
+ return alignment;\r
+ }\r
+ /**\r
+ * @param alignment the alignment to set\r
+ */\r
+ public void setAlignment(AlignmentI alignment) {\r
+ this.alignment = alignment;\r
+ }\r
+ /**\r
+ * @return the caseSensitive\r
+ */\r
+ public boolean isCaseSensitive() {\r
+ return caseSensitive;\r
+ }\r
+ /**\r
+ * @param caseSensitive the caseSensitive to set\r
+ */\r
+ public void setCaseSensitive(boolean caseSensitive) {\r
+ this.caseSensitive = caseSensitive;\r
+ }\r
+ /**\r
+ * @return the findAll\r
+ */\r
+ public boolean isFindAll() {\r
+ return findAll;\r
+ }\r
+ /**\r
+ * @param findAll the findAll to set\r
+ */\r
+ public void setFindAll(boolean findAll) {\r
+ this.findAll = findAll;\r
+ }\r
+ /**\r
+ * @return the selection\r
+ */\r
+ public jalview.datamodel.SequenceGroup getSelection() {\r
+ return selection;\r
+ }\r
+ /**\r
+ * @param selection the selection to set\r
+ */\r
+ public void setSelection(jalview.datamodel.SequenceGroup selection) {\r
+ this.selection = selection;\r
+ }\r
+ /**\r
+ * @return the idMatch\r
+ */\r
+ public Vector getIdMatch() {\r
+ return idMatch;\r
+ }\r
+ /**\r
+ * @return the regex\r
+ */\r
+ public com.stevesoft.pat.Regex getRegex() {\r
+ return regex;\r
+ }\r
+ /**\r
+ * @return the searchResults\r
+ */\r
+ public SearchResults getSearchResults() {\r
+ return searchResults;\r
+ }\r
+\r
+ /**\r
+ * @return the resIndex\r
+ */\r
+ public int getResIndex() {\r
+ return resIndex;\r
+ }\r
+\r
+ /**\r
+ * @param resIndex the resIndex to set\r
+ */\r
+ public void setResIndex(int resIndex) {\r
+ this.resIndex = resIndex;\r
+ }\r
+\r
+ /**\r
+ * @return the seqIndex\r
+ */\r
+ public int getSeqIndex() {\r
+ return seqIndex;\r
+ }\r
+\r
+ /**\r
+ * @param seqIndex the seqIndex to set\r
+ */\r
+ public void setSeqIndex(int seqIndex) {\r
+ this.seqIndex = seqIndex;\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / commitdiff