X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=41478d68c25712a0cc9cb2e9ac26bf100fed0539;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=528046734a68d7695bf242073c4de514411c3009;hpb=9a41fb8b4495359ca25aa0bbdd1e3bc500b2cdf2;p=jalview.git diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java index 5280467..41478d6 100644 --- a/src/jalview/analysis/Finder.java +++ b/src/jalview/analysis/Finder.java @@ -1,3 +1,20 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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 . + */ package jalview.analysis; import java.util.*; @@ -10,24 +27,41 @@ 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; + 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) + int seqIndex, int resIndex) { this(alignment, selectionGroup); this.seqIndex = seqIndex; @@ -42,41 +76,21 @@ public class Finder 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(); - ////// 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)) + if ((selection.getSize() < 1) + || ((selection.getEndRes() - selection.getStartRes()) < 2)) { selection = null; } @@ -85,26 +99,60 @@ public class Finder while (!found && (seqIndex < end)) { seq = (Sequence) alignment.getSequenceAt(seqIndex); - - if ( (selection != null) && !selection.getSequences(null).contains(seq)) + + if ((selection != null && selection.getSize() > 0) + && !selection.getSequences(null).contains(seq)) { seqIndex++; - resIndex = 0; + 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; + } + } + } item = seq.getSequenceAsString(); - if(!caseSensitive) - item = item.toUpperCase(); - if ( (selection != null) && - (selection.getEndRes() < alignment.getWidth() - 1)) + 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 + // /Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not StringBuffer noGapsSB = new StringBuffer(); int insertCount = 0; Vector spaces = new Vector(); @@ -131,22 +179,21 @@ public class Finder { resIndex = regex.matchedFrom(); - if ( (selection != null) && - ( (resIndex + - Integer.parseInt(spaces.elementAt(resIndex).toString())) < - selection.getStartRes())) + if ((selection != null && selection.getSize() > 0) + && ((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())); + 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; @@ -170,18 +217,16 @@ public class Finder if (!found) { seqIndex++; - resIndex = 0; + resIndex = -1; } } - for (int id = 0; id < alignment.getHeight(); id++) - { - if (regex.search(alignment.getSequenceAt(id).getName())) - { - idMatch.addElement(alignment.getSequenceAt(id)); - hasResults = true; - } - } + /** + * 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; } @@ -194,7 +239,8 @@ public class Finder } /** - * @param alignment the alignment to set + * @param alignment + * the alignment to set */ public void setAlignment(AlignmentI alignment) { @@ -210,7 +256,8 @@ public class Finder } /** - * @param caseSensitive the caseSensitive to set + * @param caseSensitive + * the caseSensitive to set */ public void setCaseSensitive(boolean caseSensitive) { @@ -226,7 +273,8 @@ public class Finder } /** - * @param findAll the findAll to set + * @param findAll + * the findAll to set */ public void setFindAll(boolean findAll) { @@ -242,7 +290,8 @@ public class Finder } /** - * @param selection the selection to set + * @param selection + * the selection to set */ public void setSelection(jalview.datamodel.SequenceGroup selection) { @@ -282,7 +331,8 @@ public class Finder } /** - * @param resIndex the resIndex to set + * @param resIndex + * the resIndex to set */ public void setResIndex(int resIndex) { @@ -298,7 +348,8 @@ public class Finder } /** - * @param seqIndex the seqIndex to set + * @param seqIndex + * the seqIndex to set */ public void setSeqIndex(int seqIndex) {