X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=9d3e6db930ab5688972d73748b3e9e67e8ff9f08;hb=fa129d373443b56d8a59fdec3a87f6f14b1771f3;hp=11a5ab38681013ff4143d73d22be810103e46c45;hpb=04b756e96e1bfdfdb823b9857240837914135536;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 11a5ab3..9d3e6db 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview. * - * 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. + * 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. * - * 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 + * 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.datamodel; @@ -46,18 +45,27 @@ public class SequenceGroup boolean displayText = true; boolean colourText = false; + + /** + * after Olivier's non-conserved only character display + */ + boolean showUnconserved = false; + /** * group members */ private Vector sequences = new Vector(); + /** * representative sequence for this group (if any) */ private SequenceI seqrep = null; + int width = -1; /** - * Colourscheme applied to group if any */ + * Colourscheme applied to group if any + */ public ColourSchemeI cs; int startRes = 0; @@ -75,6 +83,24 @@ public class SequenceGroup public Color textColour2 = Color.white; /** + * consensus calculation property + */ + private boolean ignoreGapsInConsensus = true; + + /** + * consensus calculation property + */ + private boolean showSequenceLogo = false; + + /** + * @return the includeAllConsSymbols + */ + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + + /** * Creates a new SequenceGroup object. */ public SequenceGroup() @@ -92,9 +118,9 @@ public class SequenceGroup * @param displayText * @param colourText * @param start - * first column of group + * first column of group * @param end - * last column of group + * last column of group */ public SequenceGroup(Vector sequences, String groupName, ColourSchemeI scheme, boolean displayBoxes, boolean displayText, @@ -110,29 +136,35 @@ public class SequenceGroup endRes = end; recalcConservation(); } + /** * copy constructor + * * @param seqsel */ public SequenceGroup(SequenceGroup seqsel) { - if (seqsel!=null) + if (seqsel != null) { - sequences=new Vector(); + sequences = new Vector(); Enumeration sq = seqsel.sequences.elements(); - while (sq.hasMoreElements()) { - sequences.addElement(sq.nextElement()); - }; - groupName = new String(seqsel.groupName); + while (sq.hasMoreElements()) + { + sequences.addElement(sq.nextElement()); + } + ; + if (seqsel.groupName != null) + { + groupName = new String(seqsel.groupName); + } displayBoxes = seqsel.displayBoxes; displayText = seqsel.displayText; colourText = seqsel.colourText; startRes = seqsel.startRes; endRes = seqsel.endRes; - cs =seqsel.cs; - if (seqsel.description!=null) + cs = seqsel.cs; + if (seqsel.description != null) description = new String(seqsel.description); - groupName = new String(seqsel.groupName); hidecols = seqsel.hidecols; hidereps = seqsel.hidereps; idColour = seqsel.idColour; @@ -142,9 +174,10 @@ public class SequenceGroup textColour2 = seqsel.textColour2; thresholdTextColour = seqsel.thresholdTextColour; width = seqsel.width; - if (seqsel.conserve!=null) + ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus; + if (seqsel.conserve != null) { - recalcConservation(); // safer than + recalcConservation(); // safer than // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ?? } } @@ -222,7 +255,7 @@ public class SequenceGroup * If sequence ends in gaps, the end residue can be correctly calculated here * * @param seq - * SequenceI + * SequenceI * @return int */ public int findEndRes(SequenceI seq) @@ -299,7 +332,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param col - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -333,7 +366,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param col - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -372,11 +405,12 @@ public class SequenceGroup * DOCUMENT ME! * * @param name - * DOCUMENT ME! + * DOCUMENT ME! */ public void setName(String name) { groupName = name; + // TODO: URGENT: update dependent objects (annotation row) } public void setDescription(String desc) @@ -398,7 +432,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param c - * DOCUMENT ME! + * DOCUMENT ME! */ public void setConservation(Conservation c) { @@ -409,9 +443,9 @@ public class SequenceGroup * Add s to this sequence group * * @param s - * alignment sequence to be added + * alignment sequence to be added * @param recalc - * true means Group's conservation should be recalculated + * true means Group's conservation should be recalculated */ public void addSequence(SequenceI s, boolean recalc) { @@ -427,38 +461,60 @@ public class SequenceGroup } /** - * calculate residue conservation for group + * Max Gaps Threshold for performing a conservation calculation TODO: make + * this a configurable property - or global to an alignment view + */ + private int consPercGaps = 25; + + /** + * calculate residue conservation for group - but only if necessary. */ public void recalcConservation() { - if (cs == null) + if (cs == null && consensus == null && conservation == null) { return; } try { - cs.setConsensus(AAFrequency - .calculate(sequences, startRes, endRes + 1)); - - if (cs instanceof ClustalxColourScheme) + Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, + endRes + 1, showSequenceLogo); + if (consensus != null) + { + _updateConsensusRow(cnsns); + } + if (cs != null) { - ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth()); + cs.setConsensus(cnsns); + + if (cs instanceof ClustalxColourScheme) + { + ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth()); + } } - if (cs.conservationApplied()) + if ((conservation != null) + || (cs != null && cs.conservationApplied())) { Conservation c = new Conservation(groupName, ResidueProperties.propHash, 3, sequences, startRes, endRes + 1); c.calculate(); - c.verdict(false, 25); - - cs.setConservation(c); - - if (cs instanceof ClustalxColourScheme) + c.verdict(false, consPercGaps); + if (conservation != null) { - ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth()); + _updateConservationRow(c); + } + if (cs != null) + { + cs.setConservation(c); + + if (cs instanceof ClustalxColourScheme) + { + ((ClustalxColourScheme) cs) + .resetClustalX(sequences, getWidth()); + } } } } catch (java.lang.OutOfMemoryError err) @@ -469,13 +525,56 @@ public class SequenceGroup } + private void _updateConservationRow(Conservation c) + { + if (conservation == null) + { + getConservation(); + } + // update Labels + conservation.label = "Conservation for " + getName(); + conservation.description = "Conservation for group " + getName() + + " less than " + consPercGaps + "% gaps"; + // preserve width if already set + int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length + : endRes + 1) + : endRes + 1; + conservation.annotations = null; + conservation.annotations = new Annotation[aWidth]; // should be alignment + // width + c.completeAnnotations(conservation, null, startRes, endRes + 1); + } + + public Hashtable[] consensusData = null; + + private void _updateConsensusRow(Hashtable[] cnsns) + { + if (consensus == null) + { + getConsensus(); + } + consensus.label = "Consensus for " + getName(); + consensus.description = "Percent Identity"; + consensusData = cnsns; + // preserve width if already set + int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length + : endRes + 1) + : endRes + 1; + consensus.annotations = null; + consensus.annotations = new Annotation[aWidth]; // should be alignment width + + AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1, + ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container + // for + // ignoreGapsInConsensusCalculation); + } + /** - * DOCUMENT ME! - * * @param s - * DOCUMENT ME! + * sequence to either add or remove from group * @param recalc - * DOCUMENT ME! + * flag passed to delete/addSequence to indicate if group properties + * should be recalculated */ public void addOrRemove(SequenceI s, boolean recalc) { @@ -493,9 +592,9 @@ public class SequenceGroup * DOCUMENT ME! * * @param s - * DOCUMENT ME! + * DOCUMENT ME! * @param recalc - * DOCUMENT ME! + * DOCUMENT ME! */ public void deleteSequence(SequenceI s, boolean recalc) { @@ -531,7 +630,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStartRes(int i) { @@ -542,7 +641,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEndRes(int i) { @@ -563,7 +662,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -576,7 +675,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setColourText(boolean state) { @@ -597,7 +696,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setDisplayText(boolean state) { @@ -618,7 +717,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setDisplayBoxes(boolean state) { @@ -665,7 +764,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param c - * DOCUMENT ME! + * DOCUMENT ME! */ public void setOutlineColour(Color c) { @@ -684,11 +783,14 @@ public class SequenceGroup /** * - * returns the sequences in the group ordered by the ordering given by al + * returns the sequences in the group ordered by the ordering given by al. + * this used to return an array with null entries regardless, new behaviour is + * below. TODO: verify that this does not affect use in applet or application * * @param al - * Alignment - * @return SequenceI[] + * Alignment + * @return SequenceI[] intersection of sequences in group with al, ordered by + * al, or null if group does not intersect with al */ public SequenceI[] getSequencesInOrder(AlignmentI al) { @@ -705,7 +807,20 @@ public class SequenceGroup seqs[index++] = al.getSequenceAt(i); } } - + if (index == 0) + { + return null; + } + if (index < seqs.length) + { + SequenceI[] dummy = seqs; + seqs = new SequenceI[index]; + while (--index >= 0) + { + seqs[index] = dummy[index]; + dummy[index] = null; + } + } return seqs; } @@ -719,7 +834,7 @@ public class SequenceGroup /** * @param idColour - * the idColour to set + * the idColour to set */ public void setIdColour(Color idColour) { @@ -735,14 +850,17 @@ public class SequenceGroup } /** - * set the representative sequence for this group. - * Note - this affects the interpretation of the Hidereps attribute. - * @param seqrep the seqrep to set (null means no sequence representative) + * set the representative sequence for this group. Note - this affects the + * interpretation of the Hidereps attribute. + * + * @param seqrep + * the seqrep to set (null means no sequence representative) */ public void setSeqrep(SequenceI seqrep) { this.seqrep = seqrep; } + /** * * @return true if group has a sequence representative @@ -751,39 +869,48 @@ public class SequenceGroup { return seqrep != null; } + /** * visibility of rows or represented rows covered by group */ - private boolean hidereps=false; + private boolean hidereps = false; + /** - * set visibility of sequences covered by (if no sequence representative is defined) - * or represented by this group. + * set visibility of sequences covered by (if no sequence representative is + * defined) or represented by this group. + * * @param visibility */ public void setHidereps(boolean visibility) { hidereps = visibility; } + /** * - * @return true if sequences represented (or covered) by this group should be hidden + * @return true if sequences represented (or covered) by this group should be + * hidden */ public boolean isHidereps() { return hidereps; } + /** * visibility of columns intersecting this group */ - private boolean hidecols=false; + private boolean hidecols = false; + /** * set intended visibility of columns covered by this group + * * @param visibility */ public void setHideCols(boolean visibility) { hidecols = visibility; } + /** * * @return true if columns covered by group should be hidden @@ -792,26 +919,201 @@ public class SequenceGroup { return hidecols; } + /** - * create a new sequence group from the intersection of this group - * with an alignment Hashtable of hidden representatives + * create a new sequence group from the intersection of this group with an + * alignment Hashtable of hidden representatives * - * @param alignment (may not be null) - * @param hashtable (may be null) + * @param alignment + * (may not be null) + * @param hashtable + * (may be null) * @return new group containing sequences common to this group and alignment */ public SequenceGroup intersect(AlignmentI alignment, Hashtable hashtable) { SequenceGroup sgroup = new SequenceGroup(this); - Enumeration en = getSequences(hashtable).elements(); - while (en.hasMoreElements()) + SequenceI[] insect = getSequencesInOrder(alignment); + sgroup.sequences = new Vector(); + for (int s = 0; insect != null && s < insect.length; s++) { - SequenceI elem = (SequenceI) en.nextElement(); - if (alignment.getSequences().contains(elem)) + if (hashtable == null || hashtable.containsKey(insect[s])) { - sgroup.addSequence(elem, false); + sgroup.sequences.addElement(insect[s]); } } + // Enumeration en =getSequences(hashtable).elements(); + // while (en.hasMoreElements()) + // { + // SequenceI elem = (SequenceI) en.nextElement(); + // if (alignment.getSequences().contains(elem)) + // { + // sgroup.addSequence(elem, false); + // } + // } return sgroup; } + + /** + * @return the showUnconserved + */ + public boolean getShowunconserved() + { + return showUnconserved; + } + + /** + * @param showUnconserved + * the showUnconserved to set + */ + public void setShowunconserved(boolean displayNonconserved) + { + this.showUnconserved = displayNonconserved; + } + + AlignmentAnnotation consensus = null, conservation = null; + + /** + * flag indicating if consensus histogram should be rendered + */ + private boolean showConsensusHistogram; + + /** + * + * @return automatically calculated consensus row + */ + public AlignmentAnnotation getConsensus() + { + // TODO get or calculate and get consensus annotation row for this group + int aWidth = this.getWidth(); + // pointer + // possibility + // here. + if (aWidth < 0) + { + return null; + } + if (consensus == null) + { + consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f, + 100f, AlignmentAnnotation.BAR_GRAPH); + } + consensus.hasText = true; + consensus.autoCalculated = true; + consensus.groupRef = this; + consensus.label = "Consensus for " + getName(); + consensus.description = "Percent Identity"; + return consensus; + } + + /** + * get the conservation annotation row for this group + * + * @return autoCalculated annotation row + */ + public AlignmentAnnotation getConservationRow() + { + if (conservation == null) + { + conservation = new AlignmentAnnotation("", "", new Annotation[1], 0f, + 11f, AlignmentAnnotation.BAR_GRAPH); + } + + conservation.hasText = true; + conservation.autoCalculated = true; + conservation.groupRef = this; + conservation.label = "Conservation for " + getName(); + conservation.description = "Conservation for group " + getName() + + " less than " + consPercGaps + "% gaps"; + return conservation; + } + + /** + * + * @return true if annotation rows have been instantiated for this group + */ + public boolean hasAnnotationRows() + { + return consensus != null || conservation != null; + } + + public SequenceI getConsensusSeq() + { + getConsensus(); + StringBuffer seqs = new StringBuffer(); + for (int i = 0; i < consensus.annotations.length; i++) + { + if (consensus.annotations[i] != null) + { + if (consensus.annotations[i].description.charAt(0) == '[') + { + seqs.append(consensus.annotations[i].description.charAt(1)); + } + else + { + seqs.append(consensus.annotations[i].displayCharacter); + } + } + } + + SequenceI sq = new Sequence("Group" + getName() + " Consensus", seqs + .toString()); + sq.setDescription("Percentage Identity Consensus " + + ((ignoreGapsInConsensus) ? " without gaps" : "")); + return sq; + } + + public void setIgnoreGapsConsensus(boolean state) + { + if (this.ignoreGapsInConsensus != state && consensus != null) + { + ignoreGapsInConsensus = state; + recalcConservation(); + } + ignoreGapsInConsensus = state; + } + + public boolean getIgnoreGapsConsensus() + { + return ignoreGapsInConsensus; + } + + /** + * @param includeAllConsSymbols + * the includeAllConsSymbols to set + */ + public void setIncludeAllConsSymbols(boolean includeAllConsSymbols) + { + if (this.showSequenceLogo != includeAllConsSymbols && consensus != null) + { + this.showSequenceLogo = includeAllConsSymbols; + recalcConservation(); + } + this.showSequenceLogo = includeAllConsSymbols; + } + + /** + * + * @param showConsHist + * flag indicating if the consensus histogram for this group should + * be rendered + */ + public void setShowConsensusHistogram(boolean showConsHist) + { + + if (showConsensusHistogram != showConsHist && consensus != null) + { + this.showConsensusHistogram = showConsHist; + recalcConservation(); + } + this.showConsensusHistogram = showConsHist; + } + + /** + * @return the showConsensusHistogram + */ + public boolean isShowConsensusHistogram() + { + return showConsensusHistogram; + } }