From 0bec946ff94726b35e8b0c8508c42d3cec59ee37 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Fri, 8 May 2015 17:13:48 +0100 Subject: [PATCH] JAL-1641 refactored out view settings from Desktop.java --- src/jalview/gui/CutAndPasteTransfer.java | 5 +++-- src/jalview/gui/Desktop.java | 31 +++----------------------- src/jalview/io/JSONFile.java | 35 +++++++++++++++++++++++++----- 3 files changed, 35 insertions(+), 36 deletions(-) diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index 10aa994..6511cd8 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -23,6 +23,7 @@ package jalview.gui; import jalview.datamodel.Alignment; import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; +import jalview.io.JSONFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.jbgui.GCutAndPasteTransfer; @@ -219,9 +220,9 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer af.statusBar.setText(MessageManager .getString("label.successfully_pasted_alignment_file")); - af.setShowSeqFeatures(Desktop.isCurrentSeqFeaturesVisible()); + af.setShowSeqFeatures(JSONFile.isSeqFeaturesEnabled()); - af.changeColour(Desktop.getCurrentGlobalColourScheme()); + af.changeColour(JSONFile.getColourScheme()); af.setMenusForViewport(); try diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 5038e4d..9e5bbff 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -26,11 +26,11 @@ import jalview.bin.Cache; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; +import jalview.io.JSONFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.jbgui.GSplitFrame; import jalview.jbgui.GStructureViewer; -import jalview.schemes.ColourSchemeI; import jalview.structure.StructureSelectionManager; import jalview.util.ImageMaker; import jalview.util.MessageManager; @@ -172,10 +172,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements private static AlignFrame currentAlignFrame; - private static ColourSchemeI currentGlobalColourScheme; - - private static boolean currentSeqFeaturesVisible; - public static jalview.ws.jws1.Discoverer discoverer; public static Object[] jalviewClipboard; @@ -1029,11 +1025,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements { new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format); - viewport.setShowSequenceFeatures(isCurrentSeqFeaturesVisible()); + viewport.setShowSequenceFeatures(JSONFile.isSeqFeaturesEnabled()); AlignFrame af = viewport.getAlignPanel().alignFrame; if (af != null) { - af.changeColour(getCurrentGlobalColourScheme()); + af.changeColour(JSONFile.getColourScheme()); af.setMenusForViewport(); } } @@ -3098,26 +3094,5 @@ public class Desktop extends jalview.jbgui.GDesktop implements Desktop.currentAlignFrame = currentAlignFrame; } - public static ColourSchemeI getCurrentGlobalColourScheme() - { - return currentGlobalColourScheme; - } - - public static void setCurrentGlobalColourScheme( - ColourSchemeI currentGlobalColourScheme) - { - Desktop.currentGlobalColourScheme = currentGlobalColourScheme; - } - - public static boolean isCurrentSeqFeaturesVisible() - { - return currentSeqFeaturesVisible; - } - - public static void setCurrentSeqFeaturesVisible( - boolean currentSeqFeaturesVisible) - { - Desktop.currentSeqFeaturesVisible = currentSeqFeaturesVisible; - } } diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java index 7278157..26ffb7c 100644 --- a/src/jalview/io/JSONFile.java +++ b/src/jalview/io/JSONFile.java @@ -34,7 +34,9 @@ import org.json.simple.parser.JSONParser; public class JSONFile extends AlignFile { - private ColourSchemeI cs; + private static ColourSchemeI colourScheme; + + private static boolean seqFeaturesEnabled; private String jalviewVersion; @@ -272,12 +274,13 @@ public class JSONFile extends AlignFile .get("globalColorScheme"); Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get( "showSeqFeatures").toString()); - cs = getJalviewColorScheme(jsColourScheme); - Desktop.setCurrentSeqFeaturesVisible(showFeatures); + setColourScheme(getJalviewColorScheme(jsColourScheme)); + JSONFile.setSeqFeaturesEnabled(showFeatures); + // Desktop.setCurrentSeqFeaturesVisible(showFeatures); } seqMap = new Hashtable(); - Desktop.setCurrentGlobalColourScheme(cs); + // Desktop.setCurrentGlobalColourScheme(cs); for (Iterator sequenceIter = seqJsonArray.iterator(); sequenceIter .hasNext();) { @@ -443,8 +446,8 @@ public class JSONFile extends AlignFile public void LoadAlignmentFeatures(AlignFrame af) { - af.setShowSeqFeatures(Desktop.isCurrentSeqFeaturesVisible()); - af.changeColour(Desktop.getCurrentGlobalColourScheme()); + af.setShowSeqFeatures(JSONFile.isSeqFeaturesEnabled()); + af.changeColour(getColourScheme()); af.setMenusForViewport(); } @@ -458,6 +461,26 @@ public class JSONFile extends AlignFile this.globalColorScheme = globalColorScheme; } + public static ColourSchemeI getColourScheme() + { + return colourScheme; + } + + public static void setColourScheme(ColourSchemeI colourScheme) + { + JSONFile.colourScheme = colourScheme; + } + + public static boolean isSeqFeaturesEnabled() + { + return seqFeaturesEnabled; + } + + public static void setSeqFeaturesEnabled(boolean seqFeaturesEnabled) + { + JSONFile.seqFeaturesEnabled = seqFeaturesEnabled; + } + public class JSONExportSettings { private boolean exportSequence; -- 1.7.10.2