X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=ea4f44e2f7bc3ab40aee3dd63439053f70fbba44;hb=0b23947e2cdcd704d3f313b23ba271e43d097344;hp=71891aaef54a0baa6017984a45d965aaaac084a6;hpb=d4cf3b864ffb4d148389a3cdb788e43efd4e4b47;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 71891aa..ea4f44e 100755 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 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 @@ -29,10 +29,6 @@ import java.awt.event.*; import java.util.*; import javax.swing.*; -import java.io.FileOutputStream; -import org.jibble.epsgraphics.EpsGraphics2D; -import javax.imageio.ImageIO; -import java.awt.image.BufferedImage; import java.awt.print.*; @@ -48,7 +44,8 @@ public class PCAPanel extends GPCAPanel implements Runnable int top; RotatableCanvas rc; AlignViewport av; - SequenceI [] seqs; + AlignmentView seqstrings; + SequenceI [] seqs; /** * Creates a new PCAPanel object. @@ -62,36 +59,25 @@ public class PCAPanel extends GPCAPanel implements Runnable boolean sameLength = true; - if ((av.getSelectionGroup() != null) && - (av.getSelectionGroup().getSize() > 3)) + seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null); + if(av.getSelectionGroup()==null) { - seqs = new Sequence[av.getSelectionGroup().getSize()]; - int length = av.getSelectionGroup().getSequenceAt(0).getLength(); - for (int i = 0; i < av.getSelectionGroup().getSize(); i++) - { - seqs[i] = av.getSelectionGroup().getSequenceAt(i); - if(seqs[i].getLength()!=length) - { - sameLength = false; - break; - } - } + seqs = av.alignment.getSequencesArray(); } else { - seqs = new Sequence[av.getAlignment().getHeight()]; - int length = av.alignment.getSequenceAt(0).getLength(); - - for (int i = 0; i < av.getAlignment().getHeight(); i++) - { - seqs[i] = av.getAlignment().getSequenceAt(i); - if(seqs[i].getLength()!=length) - { - sameLength = false; - break; - } + seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + } + SeqCigar sq[]=seqstrings.getSequences(); + int length = sq[0].getWidth(); - } + for (int i = 0; i < seqs.length; i++) + { + if (sq[i].getWidth() != length) + { + sameLength = false; + break; + } } if (!sameLength) @@ -136,7 +122,7 @@ public class PCAPanel extends GPCAPanel implements Runnable public void run() { try{ - pca = new PCA(seqs); + pca = new PCA(seqstrings.getSequenceStrings(' ')); pca.run(); // Now find the component coordinates @@ -175,7 +161,6 @@ public class PCAPanel extends GPCAPanel implements Runnable rc.setPoints(points, pca.getM().rows); rc.repaint(); - seqs = null; } catch(OutOfMemoryError er) { JOptionPane.showInternalMessageDialog(Desktop.desktop, @@ -269,6 +254,67 @@ public class PCAPanel extends GPCAPanel implements Runnable printer.start(); } + public void originalSeqData_actionPerformed(ActionEvent e) + { + // this was cut'n'pasted from the equivalent TreePanel method - we should make this an abstract function of all jalview analysis windows + if (seqstrings==null) + { + jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); + return; + } + // decide if av alignment is sufficiently different to original data to warrant a new window to be created + // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs) + // or create a selection box around columns in alignment view + // test Alignment(SeqCigar[]) + Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av. + getGapCharacter()); + + + if (alAndColsel != null && alAndColsel[0]!=null) + { + // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); + + Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); + Alignment dataset = av.getAlignment().getDataset(); + if (dataset != null) + { + al.setDataset(dataset); + } + + if (true) + { + // make a new frame! + AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1], + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT +); + + //>>>This is a fix for the moment, until a better solution is found!!<<< + // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer()); + + // af.addSortByOrderMenuItem(ServiceName + " Ordering", + // msaorder); + + Desktop.addInternalFrame(af, "Original Data for " + this.title, + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + } + } + /* CutAndPasteTransfer cap = new CutAndPasteTransfer(); + for (int i = 0; i < seqs.length; i++) + { + cap.appendText(new jalview.util.Format("%-" + 15 + "s").form( + seqs[i].getName())); + cap.appendText(" " + seqstrings[i] + "\n"); + + } + + Desktop.addInternalFrame(cap, "Original Data", + 400, 400); + */ + } + + class PCAPrinter extends Thread implements Printable { @@ -313,7 +359,6 @@ public class PCAPanel extends GPCAPanel implements Runnable - /** * DOCUMENT ME! * @@ -321,79 +366,7 @@ public class PCAPanel extends GPCAPanel implements Runnable */ public void eps_actionPerformed(ActionEvent e) { - boolean accurateText = true; - - String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING", - "Prompt each time"); - - // If we need to prompt, and if the GUI is visible then - // Prompt for EPS rendering style - if (renderStyle.equalsIgnoreCase("Prompt each time") - && ! - (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true"))) - { - EPSOptions eps = new EPSOptions(); - renderStyle = eps.getValue(); - - if (renderStyle == null || eps.cancelled) - return; - - } - - if (renderStyle.equalsIgnoreCase("text")) - { - accurateText = false; - } - - int width = rc.getWidth(); - int height = rc.getHeight(); - - try - { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] - {"eps"}, - new String[] - {"Encapsulated Postscript"}, - "Encapsulated Postscript"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create EPS file from PCA"); - chooser.setToolTipText("Save"); - - int value = chooser.showSaveDialog(this); - - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) - { - return; - } - - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - - FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); - EpsGraphics2D pg = new EpsGraphics2D("PCA", out, 0, 0, width, - height); - - pg.setAccurateTextMode(accurateText); - - rc.drawBackground(pg, rc.bgColour); - rc.drawScene(pg); - - if (rc.drawAxes == true) - { - rc.drawAxes(pg); - } - - - pg.flush(); - pg.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } + makePCAImage(jalview.util.ImageMaker.EPS); } /** @@ -403,48 +376,38 @@ public class PCAPanel extends GPCAPanel implements Runnable */ public void png_actionPerformed(ActionEvent e) { + makePCAImage(jalview.util.ImageMaker.PNG); + } + + void makePCAImage(int type) + { int width = rc.getWidth(); int height = rc.getHeight(); - try - { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] - {"png"}, - new String[] - {"Portable network graphics"}, - "Portable network graphics"); - - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create PNG image from PCA"); - chooser.setToolTipText("Save"); - - int value = chooser.showSaveDialog(this); - - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) - { - return; - } + jalview.util.ImageMaker im; - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - - FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); - - BufferedImage bi = new BufferedImage(width, height, - BufferedImage.TYPE_INT_RGB); - Graphics big = bi.getGraphics(); - - big.drawImage(rc.img,0,0,this); - - ImageIO.write(bi, "png", out); - out.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } + if(type == jalview.util.ImageMaker.PNG) + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.PNG, + "Make PNG image from PCA", + width, height, + null, null); + else + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.EPS, + "Make EPS file from PCA", + width, height, + null, this.getTitle()); + + if(im.getGraphics()!=null) + { + rc.drawBackground(im.getGraphics(), Color.black); + rc.drawScene(im.getGraphics()); + if (rc.drawAxes == true) + { + rc.drawAxes(im.getGraphics()); + } + im.writeImage(); + } } - }