From 4908abbb92332aba961012da6841a3e70383c291 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 30 May 2012 09:21:22 +0100 Subject: [PATCH] formatting --- src/jalview/viewmodel/AlignmentViewport.java | 83 +++++++++++++------------- 1 file changed, 42 insertions(+), 41 deletions(-) diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index fc96f62..fcb03d8 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -1,18 +1,18 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) * 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 + * 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 + * + * 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.viewmodel; @@ -43,9 +43,9 @@ import java.util.Vector; /** * base class holding visualization and analysis attributes and common logic for * an active alignment view displayed in the GUI - * + * * @author jimp - * + * */ public abstract class AlignmentViewport implements AlignViewportI { @@ -80,6 +80,7 @@ public abstract class AlignmentViewport implements AlignViewportI globalColourScheme = cs; } + @Override public ColourSchemeI getGlobalColourScheme() { return globalColourScheme; @@ -114,10 +115,12 @@ public abstract class AlignmentViewport implements AlignViewportI */ int ConsPercGaps = 25; // JBPNote : This should be a scalable property! + @Override public int getConsPercGaps() { return ConsPercGaps; } + @Override public void setSequenceConsensusHash(Hashtable[] hconsensus) { @@ -231,6 +234,7 @@ public abstract class AlignmentViewport implements AlignViewportI return calculator.isWorking(); } + @Override public boolean isCalculationInProgress( AlignmentAnnotation alignmentAnnotation) { @@ -272,10 +276,12 @@ public abstract class AlignmentViewport implements AlignViewportI * should consensus profile be rendered by default */ protected boolean showSequenceLogo = false; + /** * should consensus profile be rendered normalised to row height */ protected boolean normaliseSequenceLogo = false; + /** * should consensus histograms be rendered by default */ @@ -284,6 +290,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * @return the showConsensusProfile */ + @Override public boolean isShowSequenceLogo() { return showSequenceLogo; @@ -350,10 +357,11 @@ public abstract class AlignmentViewport implements AlignViewportI } /** - * + * * @return flag to indicate if the consensus histogram should be rendered by * default */ + @Override public boolean isShowConsensusHistogram() { return this.showConsensusHistogram; @@ -364,7 +372,6 @@ public abstract class AlignmentViewport implements AlignViewportI */ protected boolean showUnconserved = false; - /** * when set, updateAlignment will always ensure sequences are of equal length */ @@ -395,8 +402,8 @@ public abstract class AlignmentViewport implements AlignViewportI } /** - * - * + * + * * @return null or the currently selected sequence region */ public SequenceGroup getSelectionGroup() @@ -406,10 +413,10 @@ public abstract class AlignmentViewport implements AlignViewportI /** * Set the selection group for this window. - * + * * @param sg * - group holding references to sequences in this alignment view - * + * */ public void setSelectionGroup(SequenceGroup sg) { @@ -425,6 +432,7 @@ public abstract class AlignmentViewport implements AlignViewportI } } + @Override public ColumnSelection getColumnSelection() { return colSel; @@ -480,7 +488,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * unique viewId for synchronizing state (e.g. with stored Jalview Project) - * + * */ protected String viewId = null; @@ -513,10 +521,10 @@ public abstract class AlignmentViewport implements AlignViewportI /** * checks current SelectionGroup against record of last hash value, and * updates record. - * + * * @param b * update the record of last hash value - * + * * @return true if SelectionGroup changed since last call (when b is true) */ public boolean isSelectionGroupChanged(boolean b) @@ -537,7 +545,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * checks current colsel against record of last hash value, and optionally * updates record. - * + * * @param b * update the record of last hash value * @return true if colsel changed since last call (when b is true) @@ -557,6 +565,7 @@ public abstract class AlignmentViewport implements AlignViewportI return false; } + @Override public boolean getIgnoreGapsConsensus() { return ignoreGapsInConsensusCalculation; @@ -565,7 +574,7 @@ public abstract class AlignmentViewport implements AlignViewportI // / property change stuff // JBPNote Prolly only need this in the applet version. - private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( this); protected boolean showConservation = true; @@ -574,10 +583,9 @@ public abstract class AlignmentViewport implements AlignViewportI protected boolean showConsensus = true; - /** * Property change listener for changes in alignment - * + * * @param listener * DOCUMENT ME! */ @@ -589,7 +597,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * DOCUMENT ME! - * + * * @param listener * DOCUMENT ME! */ @@ -601,7 +609,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * Property change listener for changes in alignment - * + * * @param prop * DOCUMENT ME! * @param oldvalue @@ -616,7 +624,6 @@ public abstract class AlignmentViewport implements AlignViewportI } // common hide/show column stuff - public void hideSelectedColumns() { @@ -660,7 +667,6 @@ public abstract class AlignmentViewport implements AlignViewportI hasHiddenColumns = false; } - // common hide/show seq stuff public void showAllHiddenSeqs() { @@ -715,8 +721,6 @@ public abstract class AlignmentViewport implements AlignViewportI } } - - public void hideAllSelectedSeqs() { if (selectionGroup == null || selectionGroup.getSize() < 1) @@ -730,7 +734,6 @@ public abstract class AlignmentViewport implements AlignViewportI setSelectionGroup(null); } - public void hideSequence(SequenceI[] seq) { @@ -804,7 +807,6 @@ public abstract class AlignmentViewport implements AlignViewportI * broadcast selection to any interested parties */ public abstract void sendSelection(); - public void invertColumnSelection() { @@ -815,7 +817,7 @@ public abstract class AlignmentViewport implements AlignViewportI * This method returns an array of new SequenceI objects derived from the * whole alignment or just the current selection with start and end points * adjusted - * + * * @note if you need references to the actual SequenceI objects in the * alignment or currently selected then use getSequenceSelection() * @return selection as new sequenceI objects @@ -851,7 +853,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * get the currently selected sequence objects or all the sequences in the * alignment. - * + * * @return array of references to sequence objects */ public SequenceI[] getSequenceSelection() @@ -868,13 +870,12 @@ public abstract class AlignmentViewport implements AlignViewportI 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 * columns. - * + * * @return String[] */ public jalview.datamodel.CigarArray getViewAsCigars( @@ -888,7 +889,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * return a compact representation of the current alignment selection to pass * to an analysis function - * + * * @param selectedOnly * boolean true to just return the selected view * @return AlignmentView @@ -902,7 +903,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * return a compact representation of the current alignment selection to pass * to an analysis function - * + * * @param selectedOnly * boolean true to just return the selected view * @param markGroups @@ -918,13 +919,12 @@ public abstract class AlignmentViewport implements AlignViewportI hasHiddenColumns, selectedOnly, markGroups); } - /** * 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 * columns. - * + * * @return String[] */ public String[] getViewAsString(boolean selectedRegionOnly) @@ -965,7 +965,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * return visible region boundaries within given column range - * + * * @param min * first column (inclusive, from 0) * @param max @@ -1015,6 +1015,7 @@ public abstract class AlignmentViewport implements AlignViewportI return startEnd; } + /** * @return the padGaps */ @@ -1035,7 +1036,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * apply any post-edit constraints and trigger any calculations needed after * an edit has been performed on the alignment - * + * * @param ap */ public void alignmentChanged(AlignmentViewPanel ap) -- 1.7.10.2