From 69cc05ae896ee0c80b55571919dec8a4ba31de6c Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 31 Oct 2007 17:42:12 +0000 Subject: [PATCH] javadoc --- src/jalview/datamodel/HiddenSequences.java | 559 ++++++++++++++-------------- 1 file changed, 281 insertions(+), 278 deletions(-) diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java index 0514fb8..21dcce1 100755 --- a/src/jalview/datamodel/HiddenSequences.java +++ b/src/jalview/datamodel/HiddenSequences.java @@ -1,278 +1,281 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -package jalview.datamodel; - -import java.util.*; - -public class HiddenSequences -{ - public SequenceI[] hiddenSequences; - AlignmentI alignment; - - public HiddenSequences(AlignmentI al) - { - alignment = al; - } - - public int getSize() - { - if (hiddenSequences == null) - { - return 0; - } - int count = 0; - for (int i = 0; i < hiddenSequences.length; i++) - { - if (hiddenSequences[i] != null) - { - count++; - } - } - - return count; - } - - public int getWidth() - { - int width = 0; - for (int i = 0; i < hiddenSequences.length; i++) - { - if (hiddenSequences[i] != null && hiddenSequences[i].getLength() > width) - { - width = hiddenSequences[i].getLength(); - } - } - - return width; - } - - /** - * Call this method if sequences are removed from the - * main alignment - */ - public void adjustHeightSequenceDeleted(int seqIndex) - { - if (hiddenSequences == null) - { - return; - } - - int alHeight = alignment.getHeight(); - - SequenceI[] tmp = new SequenceI[alHeight + getSize()]; - int deletionIndex = adjustForHiddenSeqs(seqIndex); - - for (int i = 0; i < hiddenSequences.length; i++) - { - if (hiddenSequences[i] == null) - { - continue; - } - - if (i > deletionIndex) - { - tmp[i - 1] = hiddenSequences[i]; - } - else - { - tmp[i] = hiddenSequences[i]; - } - } - - hiddenSequences = tmp; - - } - - /** - * Call this method if sequences are added to or removed from the - * main alignment - */ - public void adjustHeightSequenceAdded() - { - if (hiddenSequences == null) - { - return; - } - - int alHeight = alignment.getHeight(); - - SequenceI[] tmp = new SequenceI[alHeight + getSize()]; - System.arraycopy(hiddenSequences, 0, tmp, 0, hiddenSequences.length); - hiddenSequences = tmp; - } - - public void hideSequence(SequenceI sequence) - { - if (hiddenSequences == null) - { - hiddenSequences = new SequenceI[alignment.getHeight()]; - } - - int alignmentIndex = alignment.findIndex(sequence); - alignmentIndex = adjustForHiddenSeqs(alignmentIndex); - - if (hiddenSequences[alignmentIndex] != null) - { - System.out.println("ERROR!!!!!!!!!!!"); - } - - hiddenSequences[alignmentIndex] = sequence; - - alignment.deleteSequence(sequence); - } - - public Vector showAll(Hashtable hiddenReps) - { - Vector revealedSeqs = new Vector(); - for (int i = 0; i < hiddenSequences.length; i++) - { - if (hiddenSequences[i] != null) - { - Vector tmp = showSequence(i, hiddenReps); - for (int t = 0; t < tmp.size(); t++) - { - revealedSeqs.addElement(tmp.elementAt(t)); - } - } - } - return revealedSeqs; - } - - public Vector showSequence(int alignmentIndex, Hashtable hiddenReps) - { - Vector revealedSeqs = new Vector(); - SequenceI repSequence = alignment.getSequenceAt(alignmentIndex); - if (repSequence != null && - hiddenReps != null - && hiddenReps.containsKey(repSequence)) - { - hiddenReps.remove(repSequence); - revealedSeqs.addElement(repSequence); - } - - int start = adjustForHiddenSeqs(alignmentIndex - 1); - int end = adjustForHiddenSeqs(alignmentIndex); - if (end >= hiddenSequences.length) - { - end = hiddenSequences.length - 1; - } - - for (int index = end; index > start; index--) - { - SequenceI seq = hiddenSequences[index]; - hiddenSequences[index] = null; - - if (seq != null) - { - if (seq.getLength() > 0) - { - revealedSeqs.addElement(seq); - alignment.getSequences().insertElementAt(seq, alignmentIndex); - } - else - { - System.out.println(seq.getName() + " has been deleted whilst hidden"); - } - } - - } - - return revealedSeqs; - } - - public SequenceI getHiddenSequence(int alignmentIndex) - { - return hiddenSequences[alignmentIndex]; - } - - public int findIndexWithoutHiddenSeqs(int alignmentIndex) - { - int index = 0; - int hiddenSeqs = 0; - if (hiddenSequences.length <= alignmentIndex) - { - alignmentIndex = hiddenSequences.length - 1; - } - - while (index <= alignmentIndex) - { - if (hiddenSequences[index] != null) - { - hiddenSeqs++; - } - index++; - } - ; - - return (alignmentIndex - hiddenSeqs); - } - - public int adjustForHiddenSeqs(int alignmentIndex) - { - int index = 0; - int hSize = hiddenSequences.length; - while (index <= alignmentIndex && index < hSize) - { - if (hiddenSequences[index] != null) - { - alignmentIndex++; - } - index++; - } - ; - - return alignmentIndex; - } - - public AlignmentI getFullAlignment() - { - int isize = hiddenSequences.length; - SequenceI[] seq = new Sequence[isize]; - - int index = 0; - for (int i = 0; i < hiddenSequences.length; i++) - { - if (hiddenSequences[i] != null) - { - seq[i] = hiddenSequences[i]; - } - else - { - seq[i] = alignment.getSequenceAt(index); - index++; - } - } - - return new Alignment(seq); - } - - public boolean isHidden(SequenceI seq) - { - for (int i = 0; i < hiddenSequences.length; i++) - { - if (hiddenSequences[i] != null && hiddenSequences[i] == seq) - { - return true; - } - } - - return false; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program 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 2 + * of the License, or (at your option) any later version. + * + * This program 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 this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ + +package jalview.datamodel; + +import java.util.*; + +public class HiddenSequences +{ + /** + * holds a list of hidden sequences associated with an alignment. + */ + public SequenceI[] hiddenSequences; + AlignmentI alignment; + + public HiddenSequences(AlignmentI al) + { + alignment = al; + } + + public int getSize() + { + if (hiddenSequences == null) + { + return 0; + } + int count = 0; + for (int i = 0; i < hiddenSequences.length; i++) + { + if (hiddenSequences[i] != null) + { + count++; + } + } + + return count; + } + + public int getWidth() + { + int width = 0; + for (int i = 0; i < hiddenSequences.length; i++) + { + if (hiddenSequences[i] != null && hiddenSequences[i].getLength() > width) + { + width = hiddenSequences[i].getLength(); + } + } + + return width; + } + + /** + * Call this method if sequences are removed from the + * main alignment + */ + public void adjustHeightSequenceDeleted(int seqIndex) + { + if (hiddenSequences == null) + { + return; + } + + int alHeight = alignment.getHeight(); + + SequenceI[] tmp = new SequenceI[alHeight + getSize()]; + int deletionIndex = adjustForHiddenSeqs(seqIndex); + + for (int i = 0; i < hiddenSequences.length; i++) + { + if (hiddenSequences[i] == null) + { + continue; + } + + if (i > deletionIndex) + { + tmp[i - 1] = hiddenSequences[i]; + } + else + { + tmp[i] = hiddenSequences[i]; + } + } + + hiddenSequences = tmp; + + } + + /** + * Call this method if sequences are added to or removed from the + * main alignment + */ + public void adjustHeightSequenceAdded() + { + if (hiddenSequences == null) + { + return; + } + + int alHeight = alignment.getHeight(); + + SequenceI[] tmp = new SequenceI[alHeight + getSize()]; + System.arraycopy(hiddenSequences, 0, tmp, 0, hiddenSequences.length); + hiddenSequences = tmp; + } + + public void hideSequence(SequenceI sequence) + { + if (hiddenSequences == null) + { + hiddenSequences = new SequenceI[alignment.getHeight()]; + } + + int alignmentIndex = alignment.findIndex(sequence); + alignmentIndex = adjustForHiddenSeqs(alignmentIndex); + + if (hiddenSequences[alignmentIndex] != null) + { + System.out.println("ERROR!!!!!!!!!!!"); + } + + hiddenSequences[alignmentIndex] = sequence; + + alignment.deleteSequence(sequence); + } + + public Vector showAll(Hashtable hiddenReps) + { + Vector revealedSeqs = new Vector(); + for (int i = 0; i < hiddenSequences.length; i++) + { + if (hiddenSequences[i] != null) + { + Vector tmp = showSequence(i, hiddenReps); + for (int t = 0; t < tmp.size(); t++) + { + revealedSeqs.addElement(tmp.elementAt(t)); + } + } + } + return revealedSeqs; + } + + public Vector showSequence(int alignmentIndex, Hashtable hiddenReps) + { + Vector revealedSeqs = new Vector(); + SequenceI repSequence = alignment.getSequenceAt(alignmentIndex); + if (repSequence != null && + hiddenReps != null + && hiddenReps.containsKey(repSequence)) + { + hiddenReps.remove(repSequence); + revealedSeqs.addElement(repSequence); + } + + int start = adjustForHiddenSeqs(alignmentIndex - 1); + int end = adjustForHiddenSeqs(alignmentIndex); + if (end >= hiddenSequences.length) + { + end = hiddenSequences.length - 1; + } + + for (int index = end; index > start; index--) + { + SequenceI seq = hiddenSequences[index]; + hiddenSequences[index] = null; + + if (seq != null) + { + if (seq.getLength() > 0) + { + revealedSeqs.addElement(seq); + alignment.getSequences().insertElementAt(seq, alignmentIndex); + } + else + { + System.out.println(seq.getName() + " has been deleted whilst hidden"); + } + } + + } + + return revealedSeqs; + } + + public SequenceI getHiddenSequence(int alignmentIndex) + { + return hiddenSequences[alignmentIndex]; + } + + public int findIndexWithoutHiddenSeqs(int alignmentIndex) + { + int index = 0; + int hiddenSeqs = 0; + if (hiddenSequences.length <= alignmentIndex) + { + alignmentIndex = hiddenSequences.length - 1; + } + + while (index <= alignmentIndex) + { + if (hiddenSequences[index] != null) + { + hiddenSeqs++; + } + index++; + } + ; + + return (alignmentIndex - hiddenSeqs); + } + + public int adjustForHiddenSeqs(int alignmentIndex) + { + int index = 0; + int hSize = hiddenSequences.length; + while (index <= alignmentIndex && index < hSize) + { + if (hiddenSequences[index] != null) + { + alignmentIndex++; + } + index++; + } + ; + + return alignmentIndex; + } + + public AlignmentI getFullAlignment() + { + int isize = hiddenSequences.length; + SequenceI[] seq = new Sequence[isize]; + + int index = 0; + for (int i = 0; i < hiddenSequences.length; i++) + { + if (hiddenSequences[i] != null) + { + seq[i] = hiddenSequences[i]; + } + else + { + seq[i] = alignment.getSequenceAt(index); + index++; + } + } + + return new Alignment(seq); + } + + public boolean isHidden(SequenceI seq) + { + for (int i = 0; i < hiddenSequences.length; i++) + { + if (hiddenSequences[i] != null && hiddenSequences[i] == seq) + { + return true; + } + } + + return false; + } +} -- 1.7.10.2