From c424c88d659c131acbcc917fc34d89bff46f7b15 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 21 Apr 2020 10:59:19 +0100 Subject: [PATCH] JAL-3603 load annotation file from RELATIVE_URL in JS, small code tidies --- src/jalview/gui/AlignFrame.java | 7 ++- src/jalview/io/AnnotationFile.java | 93 +++++++++++------------------------- src/jalview/io/FileLoader.java | 39 +++------------ src/jalview/io/FileParse.java | 81 ++++++++++++++++++++++++++----- 4 files changed, 106 insertions(+), 114 deletions(-) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index b7ba75a..7818748 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1489,10 +1489,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.load_jalview_annotations")); - chooser.setToolTipText( - MessageManager.getString("label.load_jalview_annotations")); + String tooltip = MessageManager.getString("label.load_jalview_annotations"); + chooser.setDialogTitle(tooltip); + chooser.setToolTipText(tooltip); chooser.setResponseHandler(0, new Runnable() { @Override diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index f0f1ca3..2182b24 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -20,6 +20,17 @@ */ package jalview.io; +import java.awt.Color; +import java.io.BufferedReader; +import java.util.ArrayList; +import java.util.BitSet; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.StringTokenizer; +import java.util.Vector; + import jalview.analysis.Conservation; import jalview.api.AlignViewportI; import jalview.datamodel.AlignmentAnnotation; @@ -35,51 +46,32 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; import jalview.util.ColorUtils; -import java.awt.Color; -import java.io.BufferedReader; -import java.io.FileReader; -import java.io.InputStreamReader; -import java.io.StringReader; -import java.net.URL; -import java.util.ArrayList; -import java.util.BitSet; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.List; -import java.util.Map; -import java.util.StringTokenizer; -import java.util.Vector; - public class AnnotationFile { - public AnnotationFile() - { - init(); - } + private static final String GRAPHLINE = "GRAPHLINE"; + + private static final String COMBINE = "COMBINE"; - /** - * character used to write newlines - */ protected String newline = System.getProperty("line.separator"); + private StringBuffer text; + + private SequenceI refSeq = null; + + private String refSeqId = null; + + private long nlinesread = 0; + + private String lastread = ""; + /** - * set new line string and reset the output buffer - * - * @param nl + * Constructor */ - public void setNewlineString(String nl) + public AnnotationFile() { - newline = nl; init(); } - public String getNewlineString() - { - return newline; - } - - StringBuffer text; - private void init() { text = new StringBuffer("JALVIEW_ANNOTATION" + newline + "# Created: " @@ -642,10 +634,6 @@ public class AnnotationFile } } - SequenceI refSeq = null; - - String refSeqId = null; - public boolean annotateAlignmentView(AlignViewportI viewport, Object file, DataSourceType protocol) { @@ -682,32 +670,11 @@ public class AnnotationFile BufferedReader in = null; try { - if (sourceType == DataSourceType.FILE) - { - in = FileLoader.getBufferedReader(file); - } - else if (sourceType == DataSourceType.URL) - { - URL url = new URL(file.toString()); - in = new BufferedReader(new InputStreamReader(url.openStream())); - } - else if (sourceType == DataSourceType.PASTE) - { - in = new BufferedReader(new StringReader(file.toString())); - } - else if (sourceType == DataSourceType.CLASSLOADER) - { - java.io.InputStream is = getClass().getResourceAsStream("/" + file); - if (is != null) - { - in = new BufferedReader(new java.io.InputStreamReader(is)); - } - } + in = new FileParse().getBufferedReader(file, sourceType); if (in != null) { return parseAnnotationFrom(al, hidden, in); } - } catch (Exception ex) { ex.printStackTrace(); @@ -722,12 +689,6 @@ public class AnnotationFile return false; } - long nlinesread = 0; - - String lastread = ""; - - private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE"; - public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden, BufferedReader in) throws Exception { diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 1d5be1b..3aa433e 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -20,6 +20,13 @@ */ package jalview.io; +import java.io.File; +import java.io.IOException; +import java.util.StringTokenizer; +import java.util.Vector; + +import javax.swing.SwingUtilities; + import jalview.api.ComplexAlignFile; import jalview.api.FeatureSettingsModelI; import jalview.api.FeaturesDisplayedI; @@ -39,21 +46,8 @@ import jalview.project.Jalview2XML; import jalview.schemes.ColourSchemeI; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; -import jalview.util.Platform; import jalview.ws.utils.UrlDownloadClient; -import java.io.BufferedReader; -import java.io.ByteArrayInputStream; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.FileReader; -import java.io.IOException; -import java.io.InputStreamReader; -import java.util.StringTokenizer; -import java.util.Vector; - -import javax.swing.SwingUtilities; - public class FileLoader implements Runnable { String file; @@ -641,23 +635,4 @@ public class FileLoader implements Runnable return tempStructFile.toString(); } - /** - * - * @param file a File, or a String which is a name of a file - * @return - * @throws FileNotFoundException - */ - public static BufferedReader getBufferedReader(Object file) throws FileNotFoundException { - if (file instanceof String) - { - return new BufferedReader(new FileReader((String) file)); - } - byte[] bytes = Platform.getFileBytes((File) file); - if (bytes != null) - { - return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes))); - } - return new BufferedReader(new FileReader((File) file)); - } - } diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index 13c0f43..a5a4e36 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -20,13 +20,6 @@ */ package jalview.io; -import jalview.api.AlignExportSettingsI; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureSettingsModelI; -import jalview.util.MessageManager; -import jalview.util.Platform; - import java.io.BufferedReader; import java.io.ByteArrayInputStream; import java.io.File; @@ -41,6 +34,13 @@ import java.net.MalformedURLException; import java.net.URL; import java.util.zip.GZIPInputStream; +import jalview.api.AlignExportSettingsI; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsModelI; +import jalview.util.MessageManager; +import jalview.util.Platform; + /** * implements a random access wrapper around a particular datasource, for * passing to identifyFile and AlignFile objects. @@ -332,7 +332,7 @@ public class FileParse } private void parse(File file, String fileStr, DataSourceType sourceType, - boolean isFileObject) throws MalformedURLException, IOException + boolean isFileObject) throws IOException { bytes = Platform.getFileBytes(file); dataSourceType = sourceType; @@ -373,7 +373,8 @@ public class FileParse { // BH 2018 hack for no support for access-origin bytes = Platform.getFileAsBytes(fileStr); - dataIn = new BufferedReader(new java.io.InputStreamReader(new ByteArrayInputStream(bytes))); + dataIn = new BufferedReader( + new InputStreamReader(new ByteArrayInputStream(bytes))); dataName = fileStr; } @@ -423,8 +424,7 @@ public class FileParse else if (sourceType == DataSourceType.CLASSLOADER) { errormessage = "RESOURCE CANNOT BE LOCATED"; - java.io.InputStream is = getClass() - .getResourceAsStream("/" + fileStr); + InputStream is = getClass().getResourceAsStream("/" + fileStr); if (is == null) { String suffixLess = extractSuffix(fileStr); @@ -435,7 +435,7 @@ public class FileParse } if (is != null) { - dataIn = new BufferedReader(new java.io.InputStreamReader(is)); + dataIn = new BufferedReader(new InputStreamReader(is)); dataName = fileStr; } else @@ -669,4 +669,61 @@ public class FileParse { return dataSourceType; } + + /** + * Returns a buffered reader for the input object. Returns null, or throws + * IOException, on failure. + * + * @param file + * a File, or a String which is a name of a file + * @param sourceType + * @return + * @throws IOException + */ + public BufferedReader getBufferedReader(Object file, + DataSourceType sourceType) throws IOException + { + BufferedReader in = null; + byte[] bytes; + + switch (sourceType) + { + case FILE: + if (file instanceof String) + { + return new BufferedReader(new FileReader((String) file)); + } + bytes = Platform.getFileBytes((File) file); + if (bytes != null) + { + return new BufferedReader( + new InputStreamReader(new ByteArrayInputStream(bytes))); + } + return new BufferedReader(new FileReader((File) file)); + case URL: + URL url = new URL(file.toString()); + in = new BufferedReader(new InputStreamReader(url.openStream())); + break; + case RELATIVE_URL: // JalviewJS only + bytes = Platform.getFileAsBytes(file.toString()); + if (bytes != null) + { + in = new BufferedReader( + new InputStreamReader(new ByteArrayInputStream(bytes))); + } + break; + case PASTE: + in = new BufferedReader(new StringReader(file.toString())); + break; + case CLASSLOADER: + InputStream is = getClass().getResourceAsStream("/" + file); + if (is != null) + { + in = new BufferedReader(new InputStreamReader(is)); + } + break; + } + + return in; + } } -- 1.7.10.2