X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=570241dc2f96b110d9baee421c8b74249c579335;hb=c1ffd6dd15b79a56ec0a37eebbe4df05341ca57c;hp=f59216fefc79d80fdfe9456583aca32bbea6329a;hpb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;p=jalview.git diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java index f59216f..570241d 100755 --- a/src/jalview/appletgui/Finder.java +++ b/src/jalview/appletgui/Finder.java @@ -25,14 +25,15 @@ import java.awt.*; import java.awt.event.*; import jalview.datamodel.*; +import java.awt.Rectangle; public class Finder extends Panel implements ActionListener { AlignViewport av; AlignmentPanel ap; Frame frame; - SuperGroup searchGroup; - Vector searchResults; + + SearchResults searchResults; int seqIndex = 0; int resIndex = 0; @@ -83,39 +84,40 @@ public class Finder extends Panel implements ActionListener public void createNewGroup_actionPerformed() { - Color[] newColors = new Color[24]; - for (int i = 0; i < 24; i++) - { - newColors[i] = new Color(60, 160, 115); - } - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( - newColors); - String searchString = textfield.getText(); + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null); + Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true); + dialog.add(cap); + + cap.setText(textfield.getText()); - searchGroup = new SuperGroup(searchString, ucs, true, true, false); + dialog.setBounds( frame.getLocation().x+frame.getSize().width+5, + frame.getLocation().y+20,300,100); + dialog.show(); - for (int i = 0; i < searchResults.size(); i += 3) + + String featureName = cap.getText().trim(); + if(featureName.length()<1) + return; + + + for (int i = 0; i < searchResults.getSize(); i ++ ) { - // its possible edits may have occurred since search was performed - // account for this here - - SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(searchResults. - elementAt(i).toString())); - int startRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i + - 1).toString())) - 1; - int endRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i + 2). - toString())) - 1; - - SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, - startRes, endRes); - sg.addSequence(seq, false); - av.alignment.addGroup(sg); - searchGroup.addGroup(sg); + SequenceI seq = searchResults.getResultSequence(i); + SequenceFeature sf = new SequenceFeature(featureName, + null, null, + searchResults.getResultStart(i), + searchResults.getResultEnd(i), "Search Results"); + + ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature( + featureName, new Color(60,160,115)); + seq.addSequenceFeature(sf); } - ap.av.alignment.addSuperGroup(searchGroup); + ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures(); + ap.alignFrame.sequenceFeatures.setState(true); + av.showSequenceFeatures(true); ap.highlightSearchResults(null); } @@ -123,12 +125,13 @@ public class Finder extends Panel implements ActionListener { createNewGroup.setEnabled(false); - String searchString = textfield.getText().toUpperCase(); + String searchString = textfield.getText(); + if(!caseSensitive.getState()) + searchString = searchString.toUpperCase(); com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString); - searchResults = new Vector(); - int[] allResults = null; + searchResults = new SearchResults(); Sequence seq; String item = null; @@ -149,9 +152,8 @@ public class Finder extends Panel implements ActionListener seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0)); } - searchResults.addElement(Integer.toString(av.getAlignment().findIndex(seq))); - searchResults.addElement(String.valueOf(res)); - searchResults.addElement(String.valueOf(res)); + + searchResults.addResult(seq, res, res); } catch (NumberFormatException ex) @@ -173,6 +175,7 @@ public class Finder extends Panel implements ActionListener while (!found && seqIndex < end) { + seq = (Sequence) av.alignment.getSequenceAt(seqIndex); if (selection != null && !selection.sequences.contains(seq)) @@ -182,7 +185,9 @@ public class Finder extends Panel implements ActionListener continue; } - item = seq.getSequence().toUpperCase(); + item = seq.getSequence(); + if(!caseSensitive.getState()) + item = item.toUpperCase(); if (selection != null && selection.getEndRes() < av.alignment.getWidth()) { @@ -190,7 +195,7 @@ public class Finder extends Panel implements ActionListener } ///Shall we ignore gaps???? - StringBuffer noGaps = new StringBuffer(); + StringBuffer noGapsSB = new StringBuffer(); int insertCount = 0; Vector spaces = new Vector(); @@ -199,7 +204,7 @@ public class Finder extends Panel implements ActionListener if (!jalview.util.Comparison.isGap(item.charAt(j))) { - noGaps.append(item.charAt(j)); + noGapsSB.append(item.charAt(j)); spaces.addElement(new Integer(insertCount)); } else @@ -208,10 +213,12 @@ public class Finder extends Panel implements ActionListener } } + String noGaps = noGapsSB.toString(); + for (int r = resIndex; r < noGaps.length(); r++) { - if (regex.searchFrom(noGaps.toString(), r)) + if (regex.searchFrom(noGaps, r)) { resIndex = regex.matchedFrom(); if (selection != null && @@ -221,7 +228,7 @@ public class Finder extends Panel implements ActionListener continue; } - searchResults.addElement(Integer.toString(seqIndex)); + int sres = seq.findPosition(resIndex + Integer.parseInt(spaces. elementAt(resIndex).toString())); @@ -229,8 +236,8 @@ public class Finder extends Panel implements ActionListener Integer.parseInt( spaces.elementAt(regex.matchedTo() - 1). toString())); - searchResults.addElement(sres + ""); - searchResults.addElement(eres + ""); + + searchResults.addResult(seq, sres, eres); if (!findAll) { @@ -261,34 +268,29 @@ public class Finder extends Panel implements ActionListener } } - if (searchResults.size() == 0 && idMatch.size() > 0) + if (searchResults.getSize() == 0 && idMatch.size() > 0) { ap.idPanel.highlightSearchResults(idMatch); } - if (searchResults.size() > 0) + if (searchResults.getSize() > 0) { - allResults = new int[searchResults.size()]; - for (int i = 0; i < searchResults.size(); i++) - { - allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString()); - } - createNewGroup.setEnabled(true); } else { + searchResults = null; resIndex = 0; seqIndex = 0; } // if allResults is null, this effectively switches displaySearch flag in seqCanvas - ap.highlightSearchResults(allResults); + ap.highlightSearchResults(searchResults); if (findAll) { - String message = (searchResults.size() / 3) + " matches found."; - System.out.println(message); + String message = (searchResults==null?0 : searchResults.getSize()) + " matches found."; + ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message); } } @@ -300,7 +302,7 @@ public class Finder extends Panel implements ActionListener Panel jPanel1 = new Panel(); GridLayout gridLayout1 = new GridLayout(); protected Button createNewGroup = new Button(); - + Checkbox caseSensitive = new Checkbox(); private void jbInit() throws Exception { jLabel1.setFont(new java.awt.Font("Verdana", 0, 12)); @@ -330,12 +332,15 @@ public class Finder extends Panel implements ActionListener gridLayout1.setVgap(2); createNewGroup.setEnabled(false); createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); - createNewGroup.setLabel("Create new group"); + createNewGroup.setLabel("New Feature"); createNewGroup.addActionListener(this); - jPanel1.add(findNext, null); + caseSensitive.setLabel("Match Case"); + caseSensitive.setBounds(new Rectangle(40, 49, 126, 23)); + jPanel1.add(findNext, null); jPanel1.add(findAll, null); jPanel1.add(createNewGroup, null); - this.add(textfield, null); + this.add(caseSensitive); + this.add(textfield, null); this.add(jLabel1, null); this.add(jPanel1, null); }