X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=57a14a0cc38e01ca3047bb47bc318c475c981458;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=04e855690cb435467a68485218f1300596ddf8a1;hpb=2b34ad8d6c224117ca2a3199c237fd74d8137da6;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 04e8556..57a14a0 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,19 +20,34 @@ */ package jalview.gui; -import java.util.*; -import java.awt.*; -import java.awt.event.*; -import java.awt.print.*; - -import javax.swing.*; - -import jalview.datamodel.*; -import jalview.jbgui.*; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SeqCigar; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GPCAPanel; import jalview.schemes.ResidueProperties; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.PCAModel; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Graphics; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.print.PageFormat; +import java.awt.print.Printable; +import java.awt.print.PrinterException; +import java.awt.print.PrinterJob; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JRadioButtonMenuItem; + /** * DOCUMENT ME! * @@ -43,11 +58,13 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator { + private IProgressIndicator progressBar; + RotatableCanvas rc; AlignmentPanel ap; - AlignViewport av; + AlignmentViewport av; PCAModel pcaModel; @@ -66,6 +83,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, this.av = ap.av; this.ap = ap; + progressBar = new ProgressBar(statusPanel, statusBar); + boolean sameLength = true; boolean selected = av.getSelectionGroup() != null && av.getSelectionGroup().getSize() > 0; @@ -94,11 +113,10 @@ public class PCAPanel extends GPCAPanel implements Runnable, if (!sameLength) { - JOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager.getString("label.pca_sequences_not_aligned"), - MessageManager.getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE); + JOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.getString("label.pca_sequences_not_aligned"), + MessageManager.getString("label.sequences_not_aligned"), + JOptionPane.WARNING_MESSAGE); return; } @@ -135,9 +153,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, @Override public void actionPerformed(ActionEvent e) { - if (!pcaModel.getScore_matrix().equals((String) sm)) + if (!pcaModel.getScore_matrix().equals(sm)) { - pcaModel.setScore_matrix((String) sm); + pcaModel.setScore_matrix(sm); Thread worker = new Thread(us); worker.start(); } @@ -151,7 +169,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, public void bgcolour_actionPerformed(ActionEvent e) { - Color col = JColorChooser.showDialog(this, "Select Background Colour", + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_backgroud_colour"), rc.bgColour); if (col != null) @@ -168,11 +187,11 @@ public class PCAPanel extends GPCAPanel implements Runnable, { long progId = System.currentTimeMillis(); IProgressIndicator progress = this; - String message = "Recalculating PCA"; + String message = MessageManager.getString("label.pca_recalculating"); if (getParent() == null) { progress = ap.alignFrame; - message = "Calculating PCA"; + message = MessageManager.getString("label.pca_calculating"); } progress.setProgressBar(message, progId); try @@ -378,8 +397,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, // msaorder); Desktop.addInternalFrame(af, MessageManager.formatMessage( - "label.original_data_for_params", new String[] - { this.title }), AlignFrame.DEFAULT_WIDTH, + "label.original_data_for_params", + new String[] { this.title }), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } } @@ -445,7 +464,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, */ public void eps_actionPerformed(ActionEvent e) { - makePCAImage(jalview.util.ImageMaker.EPS); + makePCAImage(jalview.util.ImageMaker.TYPE.EPS); } /** @@ -456,26 +475,34 @@ public class PCAPanel extends GPCAPanel implements Runnable, */ public void png_actionPerformed(ActionEvent e) { - makePCAImage(jalview.util.ImageMaker.PNG); + makePCAImage(jalview.util.ImageMaker.TYPE.PNG); } - void makePCAImage(int type) + void makePCAImage(jalview.util.ImageMaker.TYPE type) { int width = rc.getWidth(); int height = rc.getHeight(); jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) + if (type == jalview.util.ImageMaker.TYPE.PNG) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, - "Make PNG image from PCA", width, height, null, null); + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA", + width, height, null, null); + } + else if (type == jalview.util.ImageMaker.TYPE.EPS) + { + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA", + width, height, null, this.getTitle()); } else { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, - "Make EPS file from PCA", width, height, null, - this.getTitle()); + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", + width, height, null, this.getTitle()); + } if (im.getGraphics() != null) @@ -569,8 +596,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.points_for_params", new String[] - { this.getTitle() }), 500, 500); + "label.points_for_params", new String[] { this.getTitle() }), + 500, 500); } catch (OutOfMemoryError oom) { new OOMWarning("exporting PCA points", oom); @@ -594,8 +621,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.transformed_points_for_params", new String[] - { this.getTitle() }), 500, 500); + "label.transformed_points_for_params", + new String[] { this.getTitle() }), 500, 500); } catch (OutOfMemoryError oom) { new OOMWarning("exporting transformed PCA points", oom); @@ -603,10 +630,6 @@ public class PCAPanel extends GPCAPanel implements Runnable, } } - // methods for implementing IProgressIndicator - // need to refactor to a reusable stub class - Hashtable progressBars, progressBarHandlers; - /* * (non-Javadoc) * @@ -615,82 +638,82 @@ public class PCAPanel extends GPCAPanel implements Runnable, @Override public void setProgressBar(String message, long id) { - if (progressBars == null) - { - progressBars = new Hashtable(); - progressBarHandlers = new Hashtable(); - } - - JPanel progressPanel; - Long lId = new Long(id); - GridLayout layout = (GridLayout) statusPanel.getLayout(); - if (progressBars.get(lId) != null) - { - progressPanel = (JPanel) progressBars.get(new Long(id)); - statusPanel.remove(progressPanel); - progressBars.remove(lId); - progressPanel = null; - if (message != null) - { - statusBar.setText(message); - } - if (progressBarHandlers.contains(lId)) - { - progressBarHandlers.remove(lId); - } - layout.setRows(layout.getRows() - 1); - } - else - { - progressPanel = new JPanel(new BorderLayout(10, 5)); - - JProgressBar progressBar = new JProgressBar(); - progressBar.setIndeterminate(true); - - progressPanel.add(new JLabel(message), BorderLayout.WEST); - progressPanel.add(progressBar, BorderLayout.CENTER); - - layout.setRows(layout.getRows() + 1); - statusPanel.add(progressPanel); - - progressBars.put(lId, progressPanel); - } - // update GUI - // setMenusForViewport(); - validate(); + progressBar.setProgressBar(message, id); + // if (progressBars == null) + // { + // progressBars = new Hashtable(); + // progressBarHandlers = new Hashtable(); + // } + // + // JPanel progressPanel; + // Long lId = new Long(id); + // GridLayout layout = (GridLayout) statusPanel.getLayout(); + // if (progressBars.get(lId) != null) + // { + // progressPanel = (JPanel) progressBars.get(new Long(id)); + // statusPanel.remove(progressPanel); + // progressBars.remove(lId); + // progressPanel = null; + // if (message != null) + // { + // statusBar.setText(message); + // } + // if (progressBarHandlers.contains(lId)) + // { + // progressBarHandlers.remove(lId); + // } + // layout.setRows(layout.getRows() - 1); + // } + // else + // { + // progressPanel = new JPanel(new BorderLayout(10, 5)); + // + // JProgressBar progressBar = new JProgressBar(); + // progressBar.setIndeterminate(true); + // + // progressPanel.add(new JLabel(message), BorderLayout.WEST); + // progressPanel.add(progressBar, BorderLayout.CENTER); + // + // layout.setRows(layout.getRows() + 1); + // statusPanel.add(progressPanel); + // + // progressBars.put(lId, progressPanel); + // } + // // update GUI + // // setMenusForViewport(); + // validate(); } @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { - if (progressBarHandlers == null || !progressBars.contains(new Long(id))) - { - throw new Error( - "call setProgressBar before registering the progress bar's handler."); - } - progressBarHandlers.put(new Long(id), handler); - final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); - if (handler.canCancel()) - { - JButton cancel = new JButton( - MessageManager.getString("action.cancel")); - final IProgressIndicator us = this; - cancel.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - handler.cancelActivity(id); - us.setProgressBar( - "Cancelled " - + ((JLabel) progressPanel.getComponent(0)) - .getText(), id); - } - }); - progressPanel.add(cancel, BorderLayout.EAST); - } + progressBar.registerHandler(id, handler); + // if (progressBarHandlers == null || !progressBars.contains(new Long(id))) + // { + // throw new + // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler")); + // } + // progressBarHandlers.put(new Long(id), handler); + // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); + // if (handler.canCancel()) + // { + // JButton cancel = new JButton( + // MessageManager.getString("action.cancel")); + // final IProgressIndicator us = this; + // cancel.addActionListener(new ActionListener() + // { + // + // @Override + // public void actionPerformed(ActionEvent e) + // { + // handler.cancelActivity(id); + // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", + // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); + // } + // }); + // progressPanel.add(cancel, BorderLayout.EAST); + // } } /** @@ -700,11 +723,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, @Override public boolean operationInProgress() { - if (progressBars != null && progressBars.size() > 0) - { - return true; - } - return false; + return progressBar.operationInProgress(); } @Override