package jalview.analysis;\r
-import java.util.Vector;\r
+\r
+import java.util.*;\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
+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
- public Finder(AlignmentI alignment, SequenceGroup selectionGroup, int seqIndex, int resIndex) {\r
- this(alignment, selectionGroup);\r
- this.seqIndex=seqIndex;\r
- this.resIndex=resIndex;\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
- 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
+ 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
- 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
+ noGapsSB.append(item.charAt(j));\r
+ spaces.addElement(new Integer(insertCount));\r
}\r
- catch (NumberFormatException ex)\r
+ else\r
{\r
+ insertCount++;\r
}\r
+ }\r
\r
- ///////////////////////////////////////////////\r
-\r
- int end = alignment.getHeight();\r
+ String noGaps = noGapsSB.toString();\r
\r
+ for (int r = resIndex; r < noGaps.length(); r++)\r
+ {\r
\r
- if (selection != null)\r
+ if (regex.searchFrom(noGaps, r))\r
{\r
- if ((selection.getSize() < 1) ||\r
- ((selection.getEndRes() - selection.getStartRes()) < 2))\r
- {\r
- selection = null;\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
- 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
+ break;\r
+ }\r
\r
- for (int id = 0; id < alignment.getHeight(); id++)\r
+ r = resIndex;\r
+ }\r
+ else\r
{\r
- if (regex.search(alignment.getSequenceAt(id).getName()))\r
- {\r
- idMatch.addElement(alignment.getSequenceAt(id));\r
- hasResults=true;\r
- }\r
+ break;\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
- /**\r
- * @return the seqIndex\r
- */\r
- public int getSeqIndex() {\r
- return seqIndex;\r
+ if (!found)\r
+ {\r
+ seqIndex++;\r
+ resIndex = 0;\r
+ }\r
}\r
\r
- /**\r
- * @param seqIndex the seqIndex to set\r
- */\r
- public void setSeqIndex(int seqIndex) {\r
- this.seqIndex = seqIndex;\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
git://source.jalview.org / jalview.git / blobdiff