From b9b19b5d6d05ebc65e1e52dd78569e4c42dc317b Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 10 Jul 2015 06:18:16 +0100 Subject: [PATCH] JAL-1807 explicit imports (MCview) --- src/MCview/AppletPDBCanvas.java | 30 +++++++++++++++------------- src/MCview/AppletPDBViewer.java | 38 ++++++++++++++++++++++++++---------- src/MCview/PDBCanvas.java | 28 +++++++++++++------------- src/MCview/PDBChain.java | 12 ++++++------ src/MCview/PDBViewer.java | 41 +++++++++++++++++++++------------------ src/MCview/PDBfile.java | 6 ++++-- 6 files changed, 91 insertions(+), 64 deletions(-) diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java index dc69f43..1dfbac0 100644 --- a/src/MCview/AppletPDBCanvas.java +++ b/src/MCview/AppletPDBCanvas.java @@ -20,6 +20,20 @@ */ package MCview; +import jalview.analysis.AlignSeq; +import jalview.appletgui.AlignmentPanel; +import jalview.appletgui.FeatureRenderer; +import jalview.appletgui.SequenceRenderer; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; +import jalview.schemes.ColourSchemeI; +import jalview.structure.AtomSpec; +import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; + import java.awt.Color; import java.awt.Dimension; import java.awt.Event; @@ -37,18 +51,6 @@ import java.io.PrintStream; import java.util.List; import java.util.Vector; -import jalview.analysis.AlignSeq; -import jalview.appletgui.AlignmentPanel; -import jalview.appletgui.FeatureRenderer; -import jalview.appletgui.SequenceRenderer; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.structure.AtomSpec; -import jalview.structure.StructureListener; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; -import jalview.util.MessageManager; - public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotionListener, StructureListener { @@ -158,7 +160,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, { pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol); - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + if (protocol.equals(AppletFormatAdapter.PASTE)) { pdbentry.setFile("INLINE" + pdb.id); } @@ -543,7 +545,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, drawLabels(ig); } - public void setColours(jalview.schemes.ColourSchemeI cs) + public void setColours(ColourSchemeI cs) { bysequence = false; pdb.setColours(cs); diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java index ed13578..90a79b0 100644 --- a/src/MCview/AppletPDBViewer.java +++ b/src/MCview/AppletPDBViewer.java @@ -20,14 +20,33 @@ */ package MCview; -import java.awt.*; -import java.awt.event.*; - -import jalview.appletgui.*; -import jalview.datamodel.*; -import jalview.schemes.*; +import jalview.appletgui.AlignmentPanel; +import jalview.appletgui.CutAndPasteTransfer; +import jalview.appletgui.EmbmenuFrame; +import jalview.bin.JalviewLite; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.ZappoColourScheme; import jalview.util.MessageManager; +import java.awt.BorderLayout; +import java.awt.CheckboxGroup; +import java.awt.CheckboxMenuItem; +import java.awt.Frame; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; + public class AppletPDBViewer extends EmbmenuFrame implements ActionListener, ItemListener { @@ -52,7 +71,7 @@ public class AppletPDBViewer extends EmbmenuFrame implements StringBuffer title = new StringBuffer(seq[0].getName() + ":" + pdbcanvas.pdbentry.getFile()); - jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400); + JalviewLite.addFrame(this, title.toString(), 400, 400); } @@ -60,11 +79,10 @@ public class AppletPDBViewer extends EmbmenuFrame implements { if (evt.getSource() == mapping) { - jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer( - false, null); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, + JalviewLite.addFrame(frame, MessageManager.getString("label.pdb_sequence_mapping"), 500, 600); cap.setText(pdbcanvas.mappingDetails.toString()); diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java index 406d9f1..9a7c3c2 100644 --- a/src/MCview/PDBCanvas.java +++ b/src/MCview/PDBCanvas.java @@ -20,6 +20,19 @@ */ package MCview; +import jalview.analysis.AlignSeq; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignmentPanel; +import jalview.gui.FeatureRenderer; +import jalview.gui.SeqCanvas; +import jalview.gui.SequenceRenderer; +import jalview.io.AppletFormatAdapter; +import jalview.structure.AtomSpec; +import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; + import java.awt.Color; import java.awt.Dimension; import java.awt.Event; @@ -41,17 +54,6 @@ import java.util.Vector; import javax.swing.JPanel; import javax.swing.ToolTipManager; -import jalview.analysis.AlignSeq; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.gui.AlignmentPanel; -import jalview.gui.FeatureRenderer; -import jalview.gui.SequenceRenderer; -import jalview.structure.AtomSpec; -import jalview.structure.StructureListener; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; - public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListener, StructureListener { @@ -115,7 +117,7 @@ public class PDBCanvas extends JPanel implements MouseListener, Font font = new Font("Helvetica", Font.PLAIN, 10); - jalview.gui.SeqCanvas seqcanvas; + SeqCanvas seqcanvas; public SequenceI[] sequence; @@ -152,7 +154,7 @@ public class PDBCanvas extends JPanel implements MouseListener, { pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol); - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + if (protocol.equals(AppletFormatAdapter.PASTE)) { pdbentry.setFile("INLINE" + pdb.id); } diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 0e486ac..4e5c96b 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -20,10 +20,6 @@ */ package MCview; -import java.awt.Color; -import java.util.List; -import java.util.Vector; - import jalview.analysis.AlignSeq; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; @@ -35,6 +31,10 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.StructureMapping; +import java.awt.Color; +import java.util.List; +import java.util.Vector; + public class PDBChain { /** @@ -508,8 +508,8 @@ public class PDBChain * @param sqmpping * - mapping between destination sequence and local chain */ - public void transferResidueAnnotation( - StructureMapping mapping, jalview.datamodel.Mapping sqmpping) + public void transferResidueAnnotation(StructureMapping mapping, + Mapping sqmpping) { SequenceI sq = mapping.getSequence(); SequenceI dsq = sq; diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java index f9c7602..a0fcacf 100755 --- a/src/MCview/PDBViewer.java +++ b/src/MCview/PDBViewer.java @@ -20,12 +20,15 @@ */ package MCview; +import jalview.bin.Cache; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.gui.AlignmentPanel; +import jalview.gui.CutAndPasteTransfer; import jalview.gui.Desktop; import jalview.gui.OOMWarning; import jalview.gui.UserDefinedColours; +import jalview.io.AppletFormatAdapter; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.schemes.BuriedColourScheme; @@ -36,6 +39,7 @@ import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.UserColourScheme; import jalview.schemes.ZappoColourScheme; +import jalview.util.ImageMaker; import jalview.util.MessageManager; import jalview.ws.ebi.EBIFetchClient; @@ -52,6 +56,7 @@ import java.io.File; import java.io.FileOutputStream; import java.io.FileReader; import java.io.PrintWriter; +import java.util.Enumeration; import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; @@ -114,7 +119,7 @@ public class PDBViewer extends JInternalFrame implements Runnable { tmpPDBFile = pdbentry.getFile(); PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile, - jalview.io.AppletFormatAdapter.FILE); + AppletFormatAdapter.FILE); pdbcanvas.init(pdbentry, seq, chains, ap, protocol); @@ -379,9 +384,9 @@ public class PDBViewer extends JInternalFrame implements Runnable bg.add(buried); bg.add(user); - if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) + if (UserDefinedColours.getUserColourSchemes() != null) { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours + Enumeration userColours = UserDefinedColours .getUserColourSchemes().keys(); while (userColours.hasMoreElements()) @@ -399,7 +404,7 @@ public class PDBViewer extends JInternalFrame implements Runnable radioItem.removeActionListener(radioItem.getActionListeners()[0]); int option = JOptionPane.showInternalConfirmDialog( - jalview.gui.Desktop.desktop, + Desktop.desktop, MessageManager .getString("label.remove_from_default_list"), MessageManager @@ -407,7 +412,7 @@ public class PDBViewer extends JInternalFrame implements Runnable JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { - jalview.gui.UserDefinedColours + UserDefinedColours .removeColourFromDefaults(radioItem.getText()); coloursMenu.remove(radioItem); } @@ -500,7 +505,7 @@ public class PDBViewer extends JInternalFrame implements Runnable */ public void eps_actionPerformed(ActionEvent e) { - makePDBImage(jalview.util.ImageMaker.TYPE.EPS); + makePDBImage(ImageMaker.TYPE.EPS); } /** @@ -511,34 +516,32 @@ public class PDBViewer extends JInternalFrame implements Runnable */ public void png_actionPerformed(ActionEvent e) { - makePDBImage(jalview.util.ImageMaker.TYPE.PNG); + makePDBImage(ImageMaker.TYPE.PNG); } - void makePDBImage(jalview.util.ImageMaker.TYPE type) + void makePDBImage(ImageMaker.TYPE type) { int width = pdbcanvas.getWidth(); int height = pdbcanvas.getHeight(); - jalview.util.ImageMaker im; + ImageMaker im; - if (type == jalview.util.ImageMaker.TYPE.PNG) + if (type == ImageMaker.TYPE.PNG) { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.PNG, + im = new ImageMaker(this, ImageMaker.TYPE.PNG, "Make PNG image from view", width, height, null, null); } - else if (type == jalview.util.ImageMaker.TYPE.EPS) + else if (type == ImageMaker.TYPE.EPS) { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.EPS, + im = new ImageMaker(this, ImageMaker.TYPE.EPS, "Make EPS file from view", width, height, null, this.getTitle()); } else { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", + im = new ImageMaker(this, ImageMaker.TYPE.SVG, + "Make SVG file from PCA", width, height, null, this.getTitle()); } @@ -609,7 +612,7 @@ public class PDBViewer extends JInternalFrame implements Runnable public void mapping_actionPerformed(ActionEvent e) { - jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); + CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { cap.setText(pdbcanvas.mappingDetails.toString()); @@ -711,7 +714,7 @@ public class PDBViewer extends JInternalFrame implements Runnable public void savePDB_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file")); diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 7b7f4b0..f832fd6 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -26,7 +26,9 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.io.AlignFile; import jalview.io.FileParse; +import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; import java.awt.Color; @@ -37,7 +39,7 @@ import java.util.Hashtable; import java.util.List; import java.util.Vector; -public class PDBfile extends jalview.io.AlignFile +public class PDBfile extends AlignFile { private static String CALC_ID_PREFIX = "JalviewPDB"; @@ -531,7 +533,7 @@ public class PDBfile extends jalview.io.AlignFile } } - public void setColours(jalview.schemes.ColourSchemeI cs) + public void setColours(ColourSchemeI cs) { for (int i = 0; i < chains.size(); i++) { -- 1.7.10.2