X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=51d247d4ce659230218ca4280504b9e5f6db05f2;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=2674617886a29ea2cc69030c62f23f1561198cb5;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 2674617..51d247d 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -21,6 +21,7 @@ package jalview.gui; import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; import jalview.datamodel.SeqCigar; @@ -34,24 +35,18 @@ import jalview.viewmodel.PCAModel; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Graphics; -import java.awt.GridLayout; 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 java.util.Hashtable; import javax.swing.ButtonGroup; -import javax.swing.JButton; import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; -import javax.swing.JLabel; import javax.swing.JMenuItem; import javax.swing.JOptionPane; -import javax.swing.JPanel; -import javax.swing.JProgressBar; import javax.swing.JRadioButtonMenuItem; /** @@ -64,6 +59,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator { + private IProgressIndicator progressBar; + RotatableCanvas rc; AlignmentPanel ap; @@ -87,6 +84,8 @@ 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; @@ -115,11 +114,10 @@ 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; } @@ -142,8 +140,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, { // create an entry for this score matrix for use in PCA JCheckBoxMenuItem jm = new JCheckBoxMenuItem(); - jm.setText(MessageManager - .getStringOrReturn("label.score_model", sm)); + jm.setText(MessageManager.getStringOrReturn("label.score_model_", + sm)); jm.setSelected(pcaModel.getScore_matrix().equals(sm)); if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices .get(sm).isProtein()) @@ -170,9 +168,11 @@ public class PCAPanel extends GPCAPanel implements Runnable, } } + @Override public void bgcolour_actionPerformed(ActionEvent e) { - Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_backgroud_colour"), + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_backgroud_colour"), rc.bgColour); if (col != null) @@ -185,6 +185,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, /** * DOCUMENT ME! */ + @Override public void run() { long progId = System.currentTimeMillis(); @@ -290,6 +291,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * @param e * DOCUMENT ME! */ + @Override protected void xCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -301,6 +303,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * @param e * DOCUMENT ME! */ + @Override protected void yCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -312,11 +315,13 @@ public class PCAPanel extends GPCAPanel implements Runnable, * @param e * DOCUMENT ME! */ + @Override protected void zCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); } + @Override public void outputValues_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); @@ -332,17 +337,20 @@ public class PCAPanel extends GPCAPanel implements Runnable, } } + @Override public void showLabels_actionPerformed(ActionEvent e) { rc.showLabels(showLabels.getState()); } + @Override public void print_actionPerformed(ActionEvent e) { PCAPrinter printer = new PCAPrinter(); printer.start(); } + @Override public void originalSeqData_actionPerformed(ActionEvent e) { // this was cut'n'pasted from the equivalent TreePanel method - we should @@ -376,8 +384,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, { // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); - Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); - Alignment dataset = (av != null && av.getAlignment() != null) ? av + AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignmentI dataset = (av != null && av.getAlignment() != null) ? av .getAlignment().getDataset() : null; if (dataset != null) { @@ -399,8 +407,8 @@ 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); } } @@ -416,6 +424,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, class PCAPrinter extends Thread implements Printable { + @Override public void run() { PrinterJob printJob = PrinterJob.getPrinterJob(); @@ -435,6 +444,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, } } + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -464,6 +474,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * @param e * DOCUMENT ME! */ + @Override public void eps_actionPerformed(ActionEvent e) { makePCAImage(jalview.util.ImageMaker.TYPE.EPS); @@ -475,6 +486,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * @param e * DOCUMENT ME! */ + @Override public void png_actionPerformed(ActionEvent e) { makePCAImage(jalview.util.ImageMaker.TYPE.PNG); @@ -490,21 +502,20 @@ public class PCAPanel extends GPCAPanel implements Runnable, if (type == jalview.util.ImageMaker.TYPE.PNG) { im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.PNG, - "Make PNG image from PCA", width, height, null, null); + jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA", + width, height, null, null, null, 0, false); } 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()); + jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA", + width, height, null, this.getTitle(), null, 0, false); } else { im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", - width, height, null, this.getTitle()); + width, height, null, this.getTitle(), null, 0, false); } @@ -520,6 +531,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, } } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -555,6 +567,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = false; @@ -574,6 +587,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, itemf.setSelected(rc.applyToAllViews); itemf.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = itemf.isSelected(); @@ -590,6 +604,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent * ) */ + @Override protected void outputPoints_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); @@ -599,8 +614,8 @@ 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); @@ -615,6 +630,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event * .ActionEvent) */ + @Override protected void outputProjPoints_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); @@ -624,8 +640,8 @@ 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); @@ -633,10 +649,6 @@ public class PCAPanel extends GPCAPanel implements Runnable, } } - // methods for implementing IProgressIndicator - // need to refactor to a reusable stub class - Hashtable progressBars, progressBarHandlers; - /* * (non-Javadoc) * @@ -645,78 +657,82 @@ 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(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); - } + 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); + // } } /** @@ -726,11 +742,7 @@ 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