X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=0b4987c5eb112581a58f159c084893bff8ba3343;hb=ff7e72d6df848ca0694d25bde0e9616e8df1d18e;hp=9881b64481cfee91bd79bf3273b7eca675945e61;hpb=fa93bb578999b13c0364a712ae368ca8841012a1;p=jalview.git diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java index 9881b64..0b4987c 100755 --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -1,22 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * 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. - * - * 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 - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * 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. + * + * 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; import java.util.*; @@ -27,15 +25,17 @@ import java.awt.event.*; import jalview.commands.*; import jalview.datamodel.*; -public class RedundancyPanel - extends SliderPanel implements Runnable, WindowListener +public class RedundancyPanel extends SliderPanel implements Runnable, + WindowListener { - AlignmentPanel ap; - Stack historyList = new Stack(); // simpler than synching with alignFrame. + float[] redundancy; + SequenceI[] originalSequences; + Frame frame; + Vector redundantSeqs; public RedundancyPanel(AlignmentPanel ap) @@ -67,8 +67,8 @@ public class RedundancyPanel frame = new Frame(); frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", - 400, 100); + jalview.bin.JalviewLite.addFrame(frame, + "Redundancy threshold selection", 400, 100); frame.addWindowListener(this); @@ -77,13 +77,15 @@ public class RedundancyPanel } /** - * This is a copy of remove redundancy in jalivew.datamodel.Alignment - * except we dont want to remove redundancy, just calculate once - * so we can use the slider to dynamically hide redundant sequences - * - * @param threshold DOCUMENT ME! - * @param sel DOCUMENT ME! - * + * This is a copy of remove redundancy in jalivew.datamodel.Alignment except + * we dont want to remove redundancy, just calculate once so we can use the + * slider to dynamically hide redundant sequences + * + * @param threshold + * DOCUMENT ME! + * @param sel + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public void run() @@ -103,17 +105,17 @@ public class RedundancyPanel int start, end; - if ( (sg != null) && (sg.getSize() >= 1)) + if ((sg != null) && (sg.getSize() >= 1)) { - originalSequences = sg.getSequencesInOrder(ap.av.alignment); + originalSequences = sg.getSequencesInOrder(ap.av.getAlignment()); start = sg.getStartRes(); end = sg.getEndRes(); } else { - originalSequences = ap.av.alignment.getSequencesArray(); + originalSequences = ap.av.getAlignment().getSequencesArray(); start = 0; - end = ap.av.alignment.getWidth(); + end = ap.av.getAlignment().getWidth(); } height = originalSequences.length; @@ -124,9 +126,9 @@ public class RedundancyPanel redundancy[i] = 0f; } - // if (ap.av.hasHiddenColumns) + // if (ap.av.hasHiddenColumns) { - // omitHidden = ap.av.getSelectionAsString(); + // omitHidden = ap.av.getSelectionAsString(); } // long start = System.currentTimeMillis(); @@ -198,10 +200,7 @@ public class RedundancyPanel } ap.idPanel.idCanvas.setHighlighted(redundantSeqs); - PaintRefresher.Refresh(this, - ap.av.getSequenceSetId(), - true, - true); + PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true); } @@ -222,7 +221,8 @@ public class RedundancyPanel } } - // This has to be done before the restoreHistoryItem method of alignFrame will + // This has to be done before the restoreHistoryItem method of alignFrame + // will // actually restore these sequences. if (del.size() > 0) { @@ -239,16 +239,12 @@ public class RedundancyPanel } EditCommand cut = new EditCommand("Remove Redundancy", - EditCommand.CUT, deleted, 0, width, - ap.av.alignment); - + EditCommand.CUT, deleted, 0, width, ap.av.getAlignment()); + AlignmentI alignment=ap.av.getAlignment(); for (int i = 0; i < del.size(); i++) { - ap.av.alignment.deleteSequence(deleted[i]); - PaintRefresher.Refresh(this, - ap.av.getSequenceSetId(), - true, - true); + alignment.deleteSequence(deleted[i]); + PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true); if (sg != null) { sg.deleteSequence(deleted[i], false); @@ -259,8 +255,8 @@ public class RedundancyPanel ap.alignFrame.addHistoryItem(cut); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); } } @@ -290,15 +286,15 @@ public class RedundancyPanel { int i = Integer.parseInt(valueField.getText()); slider.setValue(i); - } - catch (Exception ex) + } catch (Exception ex) { valueField.setText(slider.getValue() + ""); } } public void windowOpened(WindowEvent evt) - {} + { + } public void windowClosing(WindowEvent evt) { @@ -306,17 +302,22 @@ public class RedundancyPanel } public void windowClosed(WindowEvent evt) - {} + { + } public void windowActivated(WindowEvent evt) - {} + { + } public void windowDeactivated(WindowEvent evt) - {} + { + } public void windowIconified(WindowEvent evt) - {} + { + } public void windowDeiconified(WindowEvent evt) - {} + { + } }