X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=ff3fe55524efcbf49e79c500a97dc24ba14e232a;hb=7423fd27a25ace181a99c20b307d54b860d0fbc2;hp=9244166344c75b7510b7d89ba52d5f0b989f474e;hpb=5d5387084823fabaff0069493688221c43dd93e7;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 9244166..ff3fe55 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.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.appletgui; @@ -117,6 +116,10 @@ public class AlignViewport AlignmentAnnotation quality; + AlignmentAnnotation[] groupConsensus; + + AlignmentAnnotation[] groupConservation; + boolean autocalculateConsensus = true; public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! @@ -148,6 +151,56 @@ public class AlignViewport this.endRes = al.getWidth() - 1; this.startSeq = 0; this.endSeq = al.getHeight() - 1; + if (applet != null) + { + // get the width and height scaling factors if they were specified + String param = applet.getParameter("widthScale"); + if (param != null) + { + try + { + widthScale = new Float(param).floatValue(); + } catch (Exception e) + { + } + if (widthScale <= 1.0) + { + System.err + .println("Invalid alignment character width scaling factor (" + + widthScale + "). Ignoring."); + widthScale = 1; + } + if (applet.debug) + { + System.err + .println("Alignment character width scaling factor is now " + + widthScale); + } + } + param = applet.getParameter("heightScale"); + if (param != null) + { + try + { + heightScale = new Float(param).floatValue(); + } catch (Exception e) + { + } + if (heightScale <= 1.0) + { + System.err + .println("Invalid alignment character height scaling factor (" + + heightScale + "). Ignoring."); + heightScale = 1; + } + if (applet.debug) + { + System.err + .println("Alignment character height scaling factor is now " + + heightScale); + } + } + } setFont(font); MAC = new jalview.util.Platform().isAMac(); @@ -201,7 +254,7 @@ public class AlignViewport param = applet.getParameter("sortByTree"); if (param != null) { - sortByTree=Boolean.valueOf(param).booleanValue(); + sortByTree = Boolean.valueOf(param).booleanValue(); } } @@ -349,7 +402,7 @@ public class AlignViewport maxR = 1.0f - minR; maxG = 0.9f - minG; maxB = 0f - minB; // scalable range for colouring both Conservation and - // Quality + // Quality float min = 0f; float max = 11f; @@ -386,7 +439,8 @@ public class AlignViewport { value = 10; } - + // TODO - refactor to use a graduatedColorScheme to calculate the + // histogram colors. float vprop = value - min; vprop /= max; conservation.annotations[i] = new Annotation(String.valueOf(c), @@ -505,37 +559,10 @@ public class AlignViewport hconsensus = new Hashtable[aWidth]; AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment - .getWidth(), hconsensus); - - for (int i = 0; i < aWidth; i++) - { - float value = 0; - if (ignoreGapsInConsensusCalculation) - { - value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)) - .floatValue(); - } - else - { - value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS)) - .floatValue(); - } - - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE) - .toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) - + " "; - - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } - - mouseOver += ((int) value + "%"); - consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', - value); - } + .getWidth(), hconsensus, true); // always calculate the full profile + AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth, + ignoreGapsInConsensusCalculation, + includeAllConsensusSymbols); if (globalColourScheme != null) { @@ -567,12 +594,6 @@ public class AlignViewport * * @return consensus sequence as a new sequence object */ - /** - * get the consensus sequence as displayed under the PID consensus annotation - * row. - * - * @return consensus sequence as a new sequence object - */ public SequenceI getConsensusSeq() { if (consensus == null) @@ -702,6 +723,8 @@ public class AlignViewport protected FeatureSettings featureSettings = null; + private float heightScale = 1, widthScale = 1; + public void setFont(Font f) { font = f; @@ -712,14 +735,14 @@ public class AlignViewport } java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font); - setCharHeight(fm.getHeight()); - charWidth = fm.charWidth('M'); + setCharHeight((int) (heightScale * fm.getHeight())); + charWidth = (int) (widthScale * fm.charWidth('M')); if (upperCasebold) { Font f2 = new Font(f.getName(), Font.BOLD, f.getSize()); fm = nullFrame.getGraphics().getFontMetrics(f2); - charWidth = fm.stringWidth("MMMMMMMMMMM") / 10; + charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)); } } @@ -946,7 +969,7 @@ public class AlignViewport * Property change listener for changes in alignment * * @param listener - * DOCUMENT ME! + * DOCUMENT ME! */ public void addPropertyChangeListener( java.beans.PropertyChangeListener listener) @@ -958,7 +981,7 @@ public class AlignViewport * DOCUMENT ME! * * @param listener - * DOCUMENT ME! + * DOCUMENT ME! */ public void removePropertyChangeListener( java.beans.PropertyChangeListener listener) @@ -970,11 +993,11 @@ public class AlignViewport * Property change listener for changes in alignment * * @param prop - * DOCUMENT ME! + * DOCUMENT ME! * @param oldvalue - * DOCUMENT ME! + * DOCUMENT ME! * @param newvalue - * DOCUMENT ME! + * DOCUMENT ME! */ public void firePropertyChange(String prop, Object oldvalue, Object newvalue) @@ -1160,6 +1183,26 @@ public class AlignViewport } /** + * get the currently selected sequence objects or all the sequences in the + * alignment. + * + * @return array of references to sequence objects + */ + public SequenceI[] getSequenceSelection() + { + SequenceI[] sequences = null; + if (selectionGroup != null) + { + sequences = selectionGroup.getSequencesInOrder(alignment); + } + if (sequences == null) + { + sequences = alignment.getSequencesArray(); + } + return sequences; + } + + /** * This method returns the visible alignment as text, as seen on the GUI, ie * if columns are hidden they will not be returned in the result. Use this for * calculating trees, PCA, redundancy etc on views which contain hidden @@ -1180,7 +1223,7 @@ public class AlignViewport seqs = selectionGroup.getSequencesInOrder(alignment); start = selectionGroup.getStartRes(); end = selectionGroup.getEndRes(); // inclusive for start and end in - // SeqCigar constructor + // SeqCigar constructor } else { @@ -1261,7 +1304,7 @@ public class AlignViewport * to an analysis function * * @param selectedOnly - * boolean true to just return the selected view + * boolean true to just return the selected view * @return AlignmentView */ jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) @@ -1487,7 +1530,6 @@ public class AlignViewport boolean centreColumnLabels; - public boolean getCentreColumnLabels() { return centreColumnLabels; @@ -1509,19 +1551,23 @@ public class AlignViewport } } } - public boolean followHighlight=false; - public boolean getFollowHighlight() { + + public boolean followHighlight = false; + + public boolean getFollowHighlight() + { return followHighlight; } + /** * show non-conserved residues only */ - public boolean showUnconserved=false; + public boolean showUnconserved = false; /** * when set, alignment should be reordered according to a newly opened tree */ - public boolean sortByTree=false; + public boolean sortByTree = false; /** * @return the showUnconserved @@ -1532,10 +1578,115 @@ public class AlignViewport } /** - * @param showUnconserved the showUnconserved to set + * @param showNonconserved + * the showUnconserved to set */ public void setShowunconserved(boolean displayNonconserved) { this.showUnconserved = displayNonconserved; } + + /** + * consensus annotation includes all percentage for all symbols in column + * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1 + * compatible) + */ + private boolean includeAllConsensusSymbols = false; + + /** + * should conservation rows be shown for groups DISABLED FOR 2.5 RELEASE (bug + * 62446) + */ + boolean showGroupConservation = false; + + /** + * should consensus rows be shown for groups DISABLED FOR 2.5 RELEASE (bug + * 62446) + */ + boolean showGroupConsensus = false; + + /** + * should consensus profile be rendered by default DISABLED FOR 2.5 RELEASE + * (bug #60064 logo rendering is not AWT 1.1 compatible) + */ + public boolean showSequenceLogo = false; + + /** + * should consensus histograms be rendered by default + */ + public boolean showConsensusHistogram = true; + + /** + * @return the showConsensusProfile + */ + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + + /** + * @param showSequenceLogo + * the new value public void setShowSequenceLogo(boolean + * showSequenceLogo) { this.showSequenceLogo = showSequenceLogo; } + */ + /** + * @param showGroupConsensus + * the showGroupConsensus to set + */ + public void setShowGroupConsensus(boolean showGroupConsensus) + { + this.showGroupConsensus = showGroupConsensus; + } + + /** + * @return the includeAllConsensusSymbols + */ + public boolean isIncludeAllConsensusSymbols() + { + return false; + } + + /** + * + * @return flag to indicate if the consensus histogram should be rendered by + * default + */ + public boolean isShowConsensusHistogram() + { + return this.showConsensusHistogram; + } + + /** + * synthesize a column selection if none exists so it covers the given + * selection group. if wholewidth is false, no column selection is made if the + * selection group covers the whole alignment width. + * + * @param sg + * @param wholewidth + */ + public void expandColSelection(SequenceGroup sg, boolean wholewidth) + { + int sgs, sge; + if (sg != null + && (sgs = sg.getStartRes()) >= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && (colSel == null || colSel.getSelected() == null || colSel + .getSelected().size() == 0)) + { + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) + { + // do nothing + return; + } + if (colSel == null) + { + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); + } + } + } + }