debian/changelog

+libjloda-java (0.0+20180317-1) experimental; urgency=medium
+
+  * New upstream commit
+    Closes: #893454
+  * Standards-Version: 4.1.3
+  * debhelper 11
+
+ -- Andreas Tille <tille@debian.org>  Tue, 20 Mar 2018 12:43:52 +0100
+
 libjloda-java (0.0+20170502-1) experimental; urgency=medium
 
   * New upstream commit

debian/compat

-9
+11

debian/control

@@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                javahelper,
                default-jdk,
                ant,
                libbatik-java,
                libjama-java,
                libopenjfx-java
-Standards-Version: 3.9.8
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libjloda-java.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libjloda-java.git
 Homepage: https://github.com/danielhuson/jloda

debian/patches/remove_applestuff.patch

@@ -44,7 +44,7 @@ Description: We are not building for Apple
 @@ -1,109 +0,0 @@
 -/**
 - * AppleStuff.java 
-- * Copyright (C) 2017 Daniel H. Huson
+- * Copyright (C) 2018 Daniel H. Huson
 - *
 - * (Some files contain contributions from other authors, who are then mentioned separately.)
 - *

src/jloda/export/EPSExportType.java

 /**
  * EPSExportType.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *
@@ -107,9 +107,9 @@ public class EPSExportType extends FileFilter implements ExportGraphicType {
      * @throws IOException
      */
     public void writeToFile(File file, final JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage) throws IOException {
-        FileOutputStream fos = new FileOutputStream(file);
+        try (FileOutputStream fos = new FileOutputStream(file)) {
         stream(imagePanel, imageScrollPane, showWholeImage, fos);
-        fos.close();
+        }
     }
 
     /**

src/jloda/export/EPSGraphics.java

 /**
  * EPSGraphics.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *

src/jloda/export/ExportGraphicType.java

 /**
  * ExportGraphicType.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *

src/jloda/export/ExportImageDialog.java

 /**
  * ExportImageDialog.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *

src/jloda/export/ExportManager.java

 /**
  * ExportManager.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *

src/jloda/export/GIFExportType.java

 /**
  * GIFExportType.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *
@@ -90,29 +90,29 @@ public class GIFExportType extends FileFilter implements ExportGraphicType {
         BufferedImage img = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
         panel.paint(img.getGraphics());
 
-        BufferedOutputStream bos = new BufferedOutputStream(out);
-        Gif89Encoder enc = new Gif89Encoder(img);
+        try (BufferedOutputStream bos = new BufferedOutputStream(out)) {
+            final Gif89Encoder enc = new Gif89Encoder(img);
             enc.setTransparentIndex(-1);
             enc.encode(bos);
-        bos.close();
+        }
     }
 
 
     public void writeToFile(File file, final JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage) throws IOException {
-        JPanel panel;
+        final JPanel panel;
         if (showWholeImage || imageScrollPane == null)
             panel = imagePanel;
         else
             panel = ExportManager.makePanelFromScrollPane(imagePanel, imageScrollPane);
 
-        Image img = imagePanel.getGraphicsConfiguration().createCompatibleImage(panel.getWidth(), panel.getHeight());
-        Graphics2D g = (Graphics2D) img.getGraphics();
+        final Image img = imagePanel.getGraphicsConfiguration().createCompatibleImage(panel.getWidth(), panel.getHeight());
+        final Graphics2D g = (Graphics2D) img.getGraphics();
         panel.paint(g);
-        BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(file));
+        try (BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(file))) {
             Gif89Encoder enc = new Gif89Encoder(img);
             enc.setTransparentIndex(-1);
             enc.encode(bos);
-        bos.close();
+        }
     }
 
     /**

src/jloda/export/GraphicsFileFilters.java

 /**
  * GraphicsFileFilters.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *

src/jloda/export/JPGExportType.java

 /**
  * JPGExportType.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *
@@ -82,12 +82,12 @@ public class JPGExportType extends FileFilter implements ExportGraphicType {
      * @throws IOException
      */
     public void stream(JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage, OutputStream out) throws IOException {
-        JPanel panel;
+        final JPanel panel;
         if (showWholeImage || imageScrollPane == null)
             panel = imagePanel;
         else
             panel = ExportManager.makePanelFromScrollPane(imagePanel, imageScrollPane);
-        BufferedImage img = new BufferedImage(panel.getWidth(), panel.getHeight(), BufferedImage.TYPE_INT_RGB);
+        final BufferedImage img = new BufferedImage(panel.getWidth(), panel.getHeight(), BufferedImage.TYPE_INT_RGB);
         panel.paint(img.getGraphics());
         ImageIO.write(img, "jpg", out);
     }
@@ -103,21 +103,20 @@ public class JPGExportType extends FileFilter implements ExportGraphicType {
      * @throws IOException
      */
     public void writeToFile(File file, final JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage) throws IOException {
-        JPanel panel;
+        final JPanel panel;
         if (showWholeImage || imageScrollPane == null)
             panel = imagePanel;
         else
             panel = ExportManager.makePanelFromScrollPane(imagePanel, imageScrollPane);
 
-        ByteArrayOutputStream out = new ByteArrayOutputStream();
-        BufferedImage img = new BufferedImage(panel.getWidth(), panel.getHeight(), BufferedImage.TYPE_INT_RGB);
+        try (ByteArrayOutputStream out = new ByteArrayOutputStream()) {
+            final BufferedImage img = new BufferedImage(panel.getWidth(), panel.getHeight(), BufferedImage.TYPE_INT_RGB);
             panel.paint(img.getGraphics());
-
             ImageIO.write(img, "jpg", out);
-
-        FileOutputStream fos = new FileOutputStream(file);
+            try (FileOutputStream fos = new FileOutputStream(file)) {
                 fos.write(out.toByteArray());
-        fos.close();
+            }
+        }
     }
 
     /**

src/jloda/export/PDFExportType.java

 /**
  * PDFExportType.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *
@@ -77,16 +77,15 @@ public class PDFExportType extends SVGExportType implements ExportGraphicType {
      * @param out   the ByteArrayOutputStream.
      */
     public static void stream(JPanel panel, OutputStream out) throws IOException {
-
         int width = panel.getWidth();
         int height = panel.getHeight();
 
         // Get the Graphics object for pdf writing
-        VectorGraphics2D pdfGraphics = new VectorGraphics2D();
+        final VectorGraphics2D pdfGraphics = new VectorGraphics2D();
         panel.paint(pdfGraphics);
 
-        PDFProcessor processor = new PDFProcessor(false);
-        Document document = processor.getDocument(pdfGraphics.getCommands(), new PageSize(width, height));
+        final PDFProcessor processor = new PDFProcessor(false);
+        final Document document = processor.getDocument(pdfGraphics.getCommands(), new PageSize(width, height));
         document.writeTo(out);
         out.flush();
     }
@@ -103,14 +102,13 @@ public class PDFExportType extends SVGExportType implements ExportGraphicType {
      * @throws java.io.IOException
      */
     public void stream(JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage, OutputStream out) throws IOException {
-        JPanel panel;
+        final JPanel panel;
         if (showWholeImage || imageScrollPane == null)
             panel = imagePanel;
         else {
             // panel=(JPanel)((JViewport)imageScrollPane.getComponent(0)).getComponent(0) ;
             panel = ExportManager.makePanelFromScrollPane(imagePanel, imageScrollPane);
         }
-
         stream(panel, out);
     }
 
@@ -125,10 +123,9 @@ public class PDFExportType extends SVGExportType implements ExportGraphicType {
      * @throws java.io.IOException
      */
     public void writeToFile(File file, final JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage) throws IOException {
-        OutputStream fos = new FileOutputStream(file);
-
+        try (OutputStream fos = new FileOutputStream(file)) {
             stream(imagePanel, imageScrollPane, showWholeImage, fos);
-        fos.close();
+        }
     }
 
     /**

src/jloda/export/PNGExportType.java

 /**
  * PNGExportType.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *
@@ -20,6 +20,7 @@
 package jloda.export;
 
 import jloda.util.Basic;
+import jloda.util.ProgramProperties;
 
 import javax.imageio.ImageIO;
 import javax.swing.*;
@@ -107,15 +108,26 @@ public class PNGExportType extends FileFilter implements ExportGraphicType {
         else
             panel = ExportManager.makePanelFromScrollPane(imagePanel, imageScrollPane);
 
-        ByteArrayOutputStream out = new ByteArrayOutputStream();
-        BufferedImage img = new BufferedImage(panel.getWidth(), panel.getHeight(), BufferedImage.TYPE_INT_RGB);
-        panel.paint(img.getGraphics());
+        try (final ByteArrayOutputStream out = new ByteArrayOutputStream()) {
+            System.err.println("(Export panel size: " + panel.getWidth() + " x " + panel.getHeight() + ")"); // todo: debugging for weird giant panel bug
+            int width = panel.getWidth();
+            int height = panel.getHeight();
+            if (width <= 0 || width >= 100000) {
+                System.err.println("Invalid width=" + width + ", setting to: " + ProgramProperties.get("PNGExportFixWidth", 1000) + " (setprop PNGExportFixWidth to change)");
+                width = ProgramProperties.get("PNGExportFixWidth", 1000);
+            }
+            if (height <= 0 || height >= 100000) {
+                System.err.println("Invalid height=" + height + ", setting to: " + ProgramProperties.get("PNGExportFixHeight", 1000) + " (setprop PNGExportFixHeight to change)");
+                height = ProgramProperties.get("PNGExportFixHeight", 1000);
+            }
 
+            final BufferedImage img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+            panel.paint(img.getGraphics());
             ImageIO.write(img, "png", out);
-
-        FileOutputStream fos = new FileOutputStream(file);
+            try (FileOutputStream fos = new FileOutputStream(file)) {
                 fos.write(out.toByteArray());
-        fos.close();
+            }
+        }
     }
 
     /**

src/jloda/export/RenderedExportType.java

 /**
  * RenderedExportType.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *
@@ -88,32 +88,33 @@ public class RenderedExportType extends FileFilter implements ExportGraphicType
      * @throws IOException
      */
     public void stream(JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage, OutputStream out) throws IOException {
-        JPanel panel;
+        final JPanel panel;
         if (showWholeImage || imageScrollPane == null)
             panel = imagePanel;
         else
             panel = ExportManager.makePanelFromScrollPane(imagePanel, imageScrollPane);
-        BufferedImage img = new BufferedImage(panel.getWidth(), panel.getHeight(), BufferedImage.TYPE_INT_RGB);
+        final BufferedImage img = new BufferedImage(panel.getWidth(), panel.getHeight(), BufferedImage.TYPE_INT_RGB);
         panel.paint(img.getGraphics());
         ImageIO.write(img, "bmp", out);
     }
 
     public void writeToFile(File file, final JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage) throws IOException {
-        JPanel panel;
+        final JPanel panel;
         if (showWholeImage || imageScrollPane == null)
             panel = imagePanel;
         else
             panel = ExportManager.makePanelFromScrollPane(imagePanel, imageScrollPane);
 
-        ByteArrayOutputStream out = new ByteArrayOutputStream();
-        BufferedImage img = new BufferedImage(panel.getWidth(), panel.getHeight(), BufferedImage.TYPE_INT_RGB);
+        try (ByteArrayOutputStream out = new ByteArrayOutputStream()) {
+            final BufferedImage img = new BufferedImage(panel.getWidth(), panel.getHeight(), BufferedImage.TYPE_INT_RGB);
             panel.paint(img.getGraphics());
 
             ImageIO.write(img, "bmp", out);
 
-        FileOutputStream fos = new FileOutputStream(file);
+            try (FileOutputStream fos = new FileOutputStream(file)) {
                 fos.write(out.toByteArray());
-        fos.close();
+            }
+        }
     }
 
     /**

src/jloda/export/SVGExportType.java

 /**
  * SVGExportType.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *
@@ -60,13 +60,12 @@ public class SVGExportType extends FileFilter implements ExportGraphicType {
     }
 
     public Object getData(JPanel panel) {
-        ByteArrayOutputStream out = new ByteArrayOutputStream();
-        try {
+        try (ByteArrayOutputStream out = new ByteArrayOutputStream()) {
             stream(panel, out);
+            return new ByteArrayInputStream(out.toByteArray());
         } catch (IOException ex) {
-            Basic.caught(ex);
+            return null;
         }
-        return new ByteArrayInputStream(out.toByteArray());
     }
 
     /**
@@ -90,20 +89,19 @@ public class SVGExportType extends FileFilter implements ExportGraphicType {
      * @throws IOException
      */
     public void stream(JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage, OutputStream out) throws IOException {
-        JPanel panel;
+        final JPanel panel;
         if (showWholeImage || imageScrollPane == null)
             panel = imagePanel;
         else
             panel = ExportManager.makePanelFromScrollPane(imagePanel, imageScrollPane);
-        DOMImplementation dom = GenericDOMImplementation.getDOMImplementation();
-        Document doc = dom.createDocument(null, "svg", null);
-        SVGGraphics2D svgGenerator = new SVGGraphics2D(doc);
+        final DOMImplementation dom = GenericDOMImplementation.getDOMImplementation();
+        final Document doc = dom.createDocument(null, "svg", null);
+        final SVGGraphics2D svgGenerator = new SVGGraphics2D(doc);
 
         panel.paint(svgGenerator);
 
         svgGenerator.stream(new OutputStreamWriter(out, "UTF-8"));
         out.flush();
-        out.close();
     }
 
     /**
@@ -117,20 +115,20 @@ public class SVGExportType extends FileFilter implements ExportGraphicType {
      * @throws IOException
      */
     public void writeToFile(File file, final JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage) throws IOException {
-        JPanel panel;
+        final JPanel panel;
         if (showWholeImage || imageScrollPane == null)
             panel = imagePanel;
         else
             panel = ExportManager.makePanelFromScrollPane(imagePanel, imageScrollPane);
 
-        DOMImplementation dom = GenericDOMImplementation.getDOMImplementation();
-        Document doc = dom.createDocument(null, "svg", null);
-        SVGGraphics2D svgGenerator = new SVGGraphics2D(doc);
+        final DOMImplementation dom = GenericDOMImplementation.getDOMImplementation();
+        final Document doc = dom.createDocument(null, "svg", null);
+        final SVGGraphics2D svgGenerator = new SVGGraphics2D(doc);
         svgGenerator.setSVGCanvasSize(panel.getSize());
         panel.paint(svgGenerator);
-        BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(file)));
+        try (BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(file)))) {
             svgGenerator.stream(bw);
-        bw.close();
+        }
     }
 
     /**

src/jloda/export/SVGStringExportType.java

 /**
  * SVGStringExportType.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *
@@ -60,7 +60,6 @@ public class SVGStringExportType implements ExportGraphicType {
     }
 
     public void stream(JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage, OutputStream out) throws IOException {
-
     }
 
     public void writeToFile(File file, JPanel imagePanel, JScrollPane imageScrollPane, boolean showWholeImage) throws IOException {

src/jloda/export/SaveImageDialog.java

 /**
  * SaveImageDialog.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *
@@ -217,6 +217,7 @@ public class SaveImageDialog extends JDialog {
                 eps.setDrawTextAsOutlines(textAsOutlines);
             }
             boolean visibleOnly = wholeImageButton == null || !wholeImageButton.isSelected();
+
             graphicsType.writeToFile(file, imagePanel, imageScrollPane, !visibleOnly);
             System.err.println("Written to file: " + file);
 

src/jloda/export/TransferableGraphic.java

 /**
  * TransferableGraphic.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *

src/jloda/export/gifEncode/DirectGif89Frame.java

 /**
  * DirectGif89Frame.java 
- * Copyright (C) 2017 Daniel H. Huson
+ * Copyright (C) 2018 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *