-1.8.3-1.3.1_FJVL
+1.8.3-1.4.0_FJVL
-1.8.3-1.3.1_JVL
+1.8.3-1.4.0_JVL
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.3.1_FJVL</version>
+ <version>1.8.3-1.4.0_FJVL</version>
</parent>
<artifactId>getdown-ant</artifactId>
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.3.1_FJVL</version>
+ <version>1.8.3-1.4.0_FJVL</version>
</parent>
<artifactId>getdown-core</artifactId>
import java.net.Proxy;
import java.net.SocketAddress;
import java.net.InetSocketAddress;
-import java.net.URI;
-import java.net.URISyntaxException;
import java.net.URL;
import java.net.URLClassLoader;
import java.net.URLConnection;
import jalview.bin.HiDPISetting;
import jalview.bin.MemorySetting;
+import jalview.util.HttpUtils;
import jalview.util.LaunchUtils;
import com.threerings.getdown.util.*;
}
}
- // test for jalview/s URL. Insert startupNotification URI into start of _appargs
+ // test for jalviewX://... URI. Insert startupNotification URI into start of _appargs
if (! StringUtil.isBlank(_jalviewUri)) {
_appargs.add(0, _jalviewUri);
}
+ /* don't convert jalviewX:// URIs to https:// URLs as Jalview can now do that
if (_appargs.size() > 0) {
- String uri = _appargs.get(0);
- try {
- log.info("TRYING TO PARSE URL '"+uri+"'");
- URI jalviewUri = new URI(uri);
- if (jalviewUri != null) {
- String scheme = jalviewUri.getScheme();
- if (scheme != null && (scheme.equals("jalview") || scheme.equals("jalviews"))) {
- boolean https = jalviewUri.getScheme().equals("jalviews");
- String host = jalviewUri.getHost();
- int port = jalviewUri.getPort();
- String file = jalviewUri.getPath();
- String ref = jalviewUri.getFragment();
- String query = jalviewUri.getQuery();
-
- _appargs.clear();
- if (host != null && host.length() > 0) {
- URL newUrl = new URL(
- (https?"https":"http")
- + "://"
- + host
- + (port > -1? String.valueOf(port) : "")
- + jalviewUri.getRawPath()
- + (query != null && query.length() > 0 ? "?" + jalviewUri.getRawQuery() : "")
- );
- _appargs.add(newUrl.toString());
- } else {
- _appargs.add(file);
- }
-
- if (ref != null && ref.length() > 0) {
- String[] refArgs = ref.split("&");
- for (String refArg : refArgs) {
- if (refArg.startsWith("jvmmempc=")) {
- jvmmempc = refArg.substring(9);
- continue;
- }
- if (refArg.startsWith("jvmmemmax=")) {
- jvmmemmax = refArg.substring(10);
- continue;
- }
- _appargs.add(URLDecoder.decode(refArg, "UTF-8"));
- }
- }
-
- }
- }
- } catch (URISyntaxException e) {
- log.error("Malformed jalview URI", uri);
+ String jalviewUri = _appargs.get(0);
+ log.info("Trying to parse uri '"+jalviewUri+"'");
+ if (HttpUtils.isJalviewSchemeUri(jalviewUri)) {
+ String jalviewUrl = HttpUtils.equivalentJalviewUrl(jalviewUri);
+ log.info("Turned url '"+jalviewUri+"' into '"+jalviewUrl+"'");
+ _appargs.clear();
+ _appargs.add(jalviewUrl);
}
}
+ */
for (String argString: _appargs) {
if (argString.startsWith("-jvmmempc=")) {
}
// almost finally check the startup file arguments
- for (File f : _startupFiles) {
- _appargs.add(f.getAbsolutePath());
- break; // Only add one file to open
+ for (String f : _startupFiles) {
+ _appargs.add(HttpUtils.startsWithHttpOrHttps(f)?f:new File(f).getAbsolutePath());
}
// check if one arg with recognised extension
{
return new File(appdir, path);
}
-
- public static void setStartupFilesFromParameterString(String p) {
+
+ public static void setStartupFilesFromParameters(List<String> parameters) {
// multiple files *might* be passed in as space separated quoted filenames
String q = "\"";
- if (!StringUtil.isBlank(p)) {
- String[] filenames;
- // split quoted params or treat as single string array
- if (p.startsWith(q) && p.endsWith(q)) {
- // this fails if, e.g.
- // p=q("stupidfilename\" " "otherfilename")
- // let's hope no-one ever ends a filename with '" '
- filenames = p.substring(q.length(),p.length()-q.length()).split(q+" "+q);
- } else {
- // single unquoted filename
- filenames = new String[]{p};
- }
-
- // check for locator file. Only allow one locator file to be double clicked (if multiple files opened, ignore locator files)
- String locatorFilename = filenames.length >= 1 ? filenames[0] : null;
- if (
- !StringUtil.isBlank(locatorFilename)
- && locatorFilename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)
- ) {
- setLocatorFile(locatorFilename);
- // remove the locator filename from the filenames array
- String[] otherFilenames = new String[filenames.length - 1];
- System.arraycopy(filenames, 1, otherFilenames, 0, otherFilenames.length);
- filenames = otherFilenames;
- }
-
- for (int i = 0; i < filenames.length; i++) {
- String filename = filenames[i];
- // skip any other locator files in a multiple file list
- if (filename.startsWith("jalview://") || filename.startsWith("jalviews://")) {
- setJalviewUri(filename);
- } else if (! filename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
+ for (String p: parameters) {
+ if (!StringUtil.isBlank(p)) {
+ String filename;
+ // split quoted params or treat as single string array
+ if (p.startsWith(q) && p.endsWith(q)) {
+ filename = p.substring(q.length(),p.length()-q.length());
+ } else {
+ // single unquoted filename
+ filename = p;
+ }
+
+ /* Now letting Jalview convert these URIs.
+ // convert jalviewX://... URLs
+ if (HttpUtils.isJalviewSchemeUri(filename)) {
+ filename = HttpUtils.equivalentJalviewUrl(filename);
+ }
+ */
+
+ // check for locator file. Only allow one locator file to be double clicked (if multiple files opened, ignore locator files)
+ if (filename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
+ // convert jalviewX://... JVL files
+ setLocatorFile(HttpUtils.equivalentJalviewUrl(filename));
+ } else {
+ // skip any other locator files in a multiple file list
addStartupFile(filename);
}
}
}
}
-
+
+ public static String getStartupFilesParameterString(List<String> parameters, boolean changeJalviewSchemeUris) {
+ StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for(String f : parameters) {
+ if (first) {
+ first = false;
+ } else {
+ sb.append(' ');
+ }
+ String p = changeJalviewSchemeUris ? HttpUtils.equivalentJalviewUrl(f) : f;
+ if (p.contains(" ")) {
+ sb.append('"');
+ sb.append(p);
+ sb.append('"');
+ } else {
+ sb.append(p);
+ }
+ }
+ return sb.toString();
+ }
+
public static void setLocatorFile(String filename) {
- _locatorFile = new File(filename);
+ _locatorFile = filename;
}
public static void addStartupFile(String filename) {
- _startupFiles.add(new File(filename));
+ _startupFiles.add(filename);
}
public static void setJalviewUri(String uri) {
try {
Config tmpConfig = null;
Map<String, Object> tmpData = new HashMap<>();
- if (_locatorFile.exists()) {
- tmpConfig = Config.parseConfig(_locatorFile, opts);
+ if (HttpUtils.startsWithHttpOrHttps(_locatorFile)) {
+ URL locatorUrl = new URL(_locatorFile);
+ try (InputStream in = ConnectionUtil.open(proxy, locatorUrl, 0, 0).getInputStream();
+ InputStreamReader reader = new InputStreamReader(in, UTF_8);
+ BufferedReader bin = new BufferedReader(reader)) {
+ tmpConfig = Config.parseConfig(bin, opts);
+ }
+ } else if (new File(_locatorFile).exists()) {
+ tmpConfig = Config.parseConfig(new File(_locatorFile), opts);
+ }
+ if (tmpConfig != null) {
// appbase is sanitised in HostWhitelist
Map<String, Object> tmpConfigData = tmpConfig.getData();
if (tmpConfig != null) {
protected static final String ENV_VAR_PREFIX = "%ENV.";
protected static final Pattern ENV_VAR_PATTERN = Pattern.compile("%ENV\\.(.*?)%");
- protected static File _locatorFile;
- protected static List<File> _startupFiles = new ArrayList<>();
+ protected static String _locatorFile;
+ protected static List<String> _startupFiles = new ArrayList<>();
protected static String _jalviewUri;
public static final String LOCATOR_FILE_EXTENSION = "jvl";
import java.util.*;
import com.threerings.getdown.util.StringUtil;
+
+import jalview.util.HttpUtils;
+
import com.threerings.getdown.data.Application;
/** Configuration that comes from our "environment" (command line args, sys props, etc.). */
int skipArgs = 2;
// Look for locator file, pass to Application and remove from appArgs
String argvLocatorFilename = argv.length > 2 ? argv[2] : null;
- if (
- !StringUtil.isBlank(argvLocatorFilename)
- && argvLocatorFilename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)
- ) {
+ if (!StringUtil.isBlank(argvLocatorFilename)
+ && argvLocatorFilename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
+ argvLocatorFilename = HttpUtils.equivalentJalviewUrl(argvLocatorFilename);
notes.add(Note.info("locatorFilename in args: '"+argv[2]+"'"));
Application.setLocatorFile(argvLocatorFilename);
package com.threerings.getdown.util;
+import static java.nio.charset.StandardCharsets.UTF_8;
+
+import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
+import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.net.MalformedURLException;
* one key/value pair in the config file was associated with the same key.
*/
public static Config parseConfig (File source, ParseOpts opts)
- throws IOException
- {
- Map<String, Object> data = new HashMap<>();
-
- // I thought that we could use HashMap<String, String[]> and put new String[] {pair[1]} for
- // the null case, but it mysteriously dies on launch, so leaving it as HashMap<String,
- // Object> for now
- for (String[] pair : parsePairs(source, opts)) {
- Object value = data.get(pair[0]);
- if (value == null) {
- data.put(pair[0], pair[1]);
- } else if (value instanceof String) {
- data.put(pair[0], new String[] { (String)value, pair[1] });
- } else if (value instanceof String[]) {
- String[] values = (String[])value;
- String[] nvalues = new String[values.length+1];
- System.arraycopy(values, 0, nvalues, 0, values.length);
- nvalues[values.length] = pair[1];
- data.put(pair[0], nvalues);
+ throws IOException
+ {
+ Map<String, Object> data = new HashMap<>();
+
+ // I thought that we could use HashMap<String, String[]> and put new String[] {pair[1]} for
+ // the null case, but it mysteriously dies on launch, so leaving it as HashMap<String,
+ // Object> for now
+ for (String[] pair : parsePairs(source, opts)) {
+ Object value = data.get(pair[0]);
+ if (value == null) {
+ data.put(pair[0], pair[1]);
+ } else if (value instanceof String) {
+ data.put(pair[0], new String[] { (String)value, pair[1] });
+ } else if (value instanceof String[]) {
+ String[] values = (String[])value;
+ String[] nvalues = new String[values.length+1];
+ System.arraycopy(values, 0, nvalues, 0, values.length);
+ nvalues[values.length] = pair[1];
+ data.put(pair[0], nvalues);
+ }
+ }
+
+ // special magic for the getdown.txt config: if the parsed data contains 'strict_comments =
+ // true' then we reparse the file with strict comments (i.e. # is only assumed to start a
+ // comment in column 0)
+ if (!opts.strictComments && Boolean.parseBoolean((String)data.get("strict_comments"))) {
+ opts.strictComments = true;
+ return parseConfig(source, opts);
}
- }
- // special magic for the getdown.txt config: if the parsed data contains 'strict_comments =
- // true' then we reparse the file with strict comments (i.e. # is only assumed to start a
- // comment in column 0)
- if (!opts.strictComments && Boolean.parseBoolean((String)data.get("strict_comments"))) {
- opts.strictComments = true;
- return parseConfig(source, opts);
+ return new Config(data);
}
- return new Config(data);
- }
+ public static Config parseConfig (Reader source, ParseOpts opts)
+ throws IOException
+ {
+ Map<String, Object> data = new HashMap<>();
+
+ // I thought that we could use HashMap<String, String[]> and put new String[] {pair[1]} for
+ // the null case, but it mysteriously dies on launch, so leaving it as HashMap<String,
+ // Object> for now
+ for (String[] pair : parsePairs(source, opts)) {
+ Object value = data.get(pair[0]);
+ if (value == null) {
+ data.put(pair[0], pair[1]);
+ } else if (value instanceof String) {
+ data.put(pair[0], new String[] { (String)value, pair[1] });
+ } else if (value instanceof String[]) {
+ String[] values = (String[])value;
+ String[] nvalues = new String[values.length+1];
+ System.arraycopy(values, 0, nvalues, 0, values.length);
+ nvalues[values.length] = pair[1];
+ data.put(pair[0], nvalues);
+ }
+ }
+
+ // special magic for the getdown.txt config: if the parsed data contains 'strict_comments =
+ // true' then we reparse the file with strict comments (i.e. # is only assumed to start a
+ // comment in column 0)
+ if (!opts.strictComments && Boolean.parseBoolean((String)data.get("strict_comments"))) {
+ opts.strictComments = true;
+ source.reset();
+ return parseConfig(source, opts);
+ }
+
+ return new Config(data);
+ }
public Config (Map<String, Object> data) {
_data = data;
--- /dev/null
+package jalview.bin;
+
+public class Console {
+ public static boolean initLogger() {
+ return false;
+ }
+ public static void outPrintln(String s) {
+ }
+ public static void errPrintln(String s) {
+ }
+}
import java.lang.management.ManagementFactory;
import java.lang.management.OperatingSystemMXBean;
+import jalview.util.ErrorLog;
+
/**
* Isolated class to ascertain physical memory of the system using
* com.sun.management.OperatingSystemMXBean class's getTotalPhysicalMemorySize
} catch (NoClassDefFoundError e)
{
// com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
- System.err.println(
+ ErrorLog.errPrintln(
"No com.sun.management.OperatingSystemMXBean: cannot get total physical memory size");
}
*/
package jalview.bin;
+import java.awt.HeadlessException;
import java.util.Locale;
-import java.awt.HeadlessException;
+import jalview.util.ErrorLog;
public class HiDPISetting
{
}
} catch (NumberFormatException e)
{
- System.err.println(setHiDPIScalePropertyName + " property give ("
+ ErrorLog.errPrintln(setHiDPIScalePropertyName + " property give ("
+ setHiDPIScaleProperty + ") but not parseable as integer");
}
}
try
{
int existingPropertyVal = Integer.parseInt(existingProperty);
- System.out.println("Existing " + scalePropertyName + " is "
+ ErrorLog.outPrintln("Existing " + scalePropertyName + " is "
+ existingPropertyVal);
if (existingPropertyVal > 1)
{
}
} catch (NumberFormatException e)
{
- System.out.println("Could not convert property " + scalePropertyName
- + " vale '" + existingProperty + "' to number");
+ ErrorLog.outPrintln(
+ "Could not convert property " + scalePropertyName
+ + " vale '" + existingProperty + "' to number");
}
}
dpi = screenInfo.getScreenResolution();
} catch (HeadlessException e)
{
- System.err.println("Cannot get screen resolution: " + e.getMessage());
+ if (isLinux)
+ {
+ ErrorLog.errPrintln(
+ "Cannot get screen resolution: " + e.getMessage());
+ }
}
// try and get screen size height and width
mindimension = Math.min(height, width);
} catch (HeadlessException e)
{
- System.err.println(
- "Cannot get screen size height and width:" + e.getMessage());
+ if (isLinux)
+ {
+ ErrorLog.errPrintln("Cannot get screen size height and width:"
+ + e.getMessage());
+ }
}
// attempt at a formula for scaling based on screen dpi and mindimension.
import java.util.Locale;
+import jalview.util.ErrorLog;
+
/**
* Methods to decide on appropriate memory setting for Jalview based on two
* optionally provided values: jvmmempc - the maximum percentage of total
*/
public class MemorySetting
{
+ // This must match the value of Arg.JVMMEMPC.getName()
public static final String MAX_HEAPSIZE_PERCENT_PROPERTY_NAME = "jvmmempc";
+ // This must match the value of Arg.JVMMEMMAX.getName()
public static final String MAX_HEAPSIZE_PROPERTY_NAME = "jvmmemmax";
private static final int MAX_HEAPSIZE_PERCENT_DEFAULT = 90; // 90%
else
{
// number too big for a Long. Limit to Long.MAX_VALUE
- System.out.println("Memory parsing of '" + memString
+ ErrorLog.outPrintln("Memory parsing of '" + memString
+ "' produces number too big. Limiting to Long.MAX_VALUE="
+ Long.MAX_VALUE);
return Long.MAX_VALUE;
ADJUSTMENT_MESSAGE = reason;
if (!quiet)
{
- System.out.println(reason);
+ ErrorLog.outPrintln(reason);
}
}
if (channelPropsURL == null)
{
// complete failure of channel_properties, set all properties to defaults
- System.err.println("Failed to find '/" + CHANNEL_PROPERTIES_FILENAME
+ ErrorLog.errPrintln("Failed to find '/" + CHANNEL_PROPERTIES_FILENAME
+ "' file at '"
+ (channelPropsURL == null ? "null"
: channelPropsURL.toString())
{
try
{
- InputStream channelPropsIS = channelPropsURL.openStream();
+ InputStream channelPropsIS = HttpUtils.openStream(channelPropsURL);
tryChannelProps.load(channelPropsIS);
channelPropsIS.close();
} catch (IOException e)
{
- System.err.println(e.getMessage());
+ ErrorLog.errPrintln(e.getMessage());
// return false;
}
}
channelProps.load(is);
} catch (FileNotFoundException e)
{
- System.err.println(e.getMessage());
+ ErrorLog.errPrintln(e.getMessage());
} catch (IOException e)
{
- System.err.println(e.getMessage());
+ ErrorLog.errPrintln(e.getMessage());
}
}
}
}
else
{
- System.err.println("Failed to get channel property '" + key + "'");
+ ErrorLog.errPrintln("Failed to get channel property '" + key + "'");
}
}
return null;
img = imgIcon == null ? null : imgIcon.getImage();
if (img == null)
{
- System.err.println(
+ ErrorLog.errPrintln(
"Failed to load channel image " + key + "=" + path);
if (!useClassDefaultImage)
{
{
return urlMap().getOrDefault(key, null);
}
- System.err.println(
+ ErrorLog.errPrintln(
"Do not use getImageURL(key) before using getImage(key...)");
}
return null;
--- /dev/null
+package jalview.util;
+
+public class ErrorLog
+{
+ private static boolean hasConsole = true;
+
+ public static void outPrintln(String message)
+ {
+ println(message, false);
+ }
+
+ public static void errPrintln(String message)
+ {
+ println(message, true);
+ }
+
+ public static void println(String message, boolean err)
+ {
+ if (hasConsole)
+ {
+ try
+ {
+ hasConsole = jalview.bin.Console.initLogger();
+ if (hasConsole)
+ {
+ if (err)
+ {
+ jalview.bin.Console.errPrintln(message);
+ }
+ else
+ {
+ jalview.bin.Console.outPrintln(message);
+ }
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ } catch (NoClassDefFoundError t)
+ {
+ hasConsole = false;
+ System.err.println(
+ "jalview.util.ErrorLog has no jalview.bin.Console. Using System.err and System.out.");
+ }
+ }
+ if (!hasConsole)
+ {
+ if (err)
+ {
+ System.err.println("jalview.util.ErrorLog: " + message);
+ }
+ else
+ {
+ System.out.println("jalview.util.ErrorLog: " + message);
+
+ }
+ }
+ }
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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
+ * 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
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.ProtocolException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
+
+public class HttpUtils
+{
+
+ /**
+ * Returns true if it is possible to open an input stream at the given URL,
+ * else false. The input stream is closed.
+ *
+ * @param url
+ * @return
+ */
+ public static boolean isValidUrl(String url)
+ {
+ InputStream is = null;
+ try
+ {
+ is = HttpUtils.openStream(new URL(url));
+ if (is != null)
+ {
+ return true;
+ }
+ } catch (IOException x)
+ {
+ // MalformedURLException, FileNotFoundException
+ return false;
+ } finally
+ {
+ if (is != null)
+ {
+ try
+ {
+ is.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ return false;
+ }
+
+ public static boolean startsWithHttpOrHttps(String file)
+ {
+ return file.startsWith("http://") || file.startsWith("https://");
+ }
+
+ /**
+ * wrapper to get/post to a URL or check headers
+ *
+ * @param url
+ * @param ids
+ * @param readTimeout
+ * @return
+ * @throws IOException
+ * @throws ProtocolException
+ */
+ public static boolean checkUrlAvailable(URL url, int readTimeout)
+ throws IOException, ProtocolException
+ {
+ // jalview.bin.Console.outPrintln(System.currentTimeMillis() + " " + url);
+
+ HttpURLConnection connection = (HttpURLConnection) url.openConnection();
+ connection.setRequestMethod("HEAD");
+ connection.setDoInput(true);
+ connection.setUseCaches(false);
+ connection.setConnectTimeout(300);
+ connection.setReadTimeout(readTimeout);
+
+ // HttpURLConnection doesn't follow redirects from http to https. It should!
+ HttpURLConnection conn = followConnection(connection);
+ return conn.getResponseCode() == 200;
+ }
+
+ /**
+ * wrapper to follow a URL connection ALLOWING redirects from http to https
+ *
+ * @param HttpURLConnection
+ * conn0
+ * @return HttpUrlConnection conn
+ */
+ public static HttpURLConnection followConnection(HttpURLConnection conn0)
+ throws IOException
+ {
+ URL url = conn0.getURL();
+ if (url == null)
+ {
+ return null;
+ }
+ HttpURLConnection conn = null;
+ int response = conn0.getResponseCode();
+ boolean followed = false;
+ if (response >= 300 && response < 400 && conn0.getFollowRedirects())
+ {
+ // we are only checking for a redirect from http to https
+ if ("http".equals(url.getProtocol()))
+ {
+ URL loc = new URL(conn0.getHeaderField("Location"));
+ if (loc != null && "https".equals(loc.getProtocol()))
+ {
+ conn = (HttpURLConnection) loc.openConnection();
+ conn.setRequestMethod(conn0.getRequestMethod());
+ conn.setDoInput(conn0.getDoInput());
+ conn.setUseCaches(conn0.getUseCaches());
+ conn.setConnectTimeout(conn0.getConnectTimeout());
+ conn.setReadTimeout(conn0.getReadTimeout());
+ conn.setInstanceFollowRedirects(
+ conn0.getInstanceFollowRedirects());
+ followed = true;
+ }
+ }
+ }
+ return followed && conn != null ? conn : conn0;
+ }
+
+ /**
+ * wrapper to follow a URL connection ALLOWING redirects from http to https
+ *
+ * @param URL
+ * url
+ * @return HttpUrlConnection conn
+ */
+ public static HttpURLConnection openConnection(URL url) throws IOException
+ {
+ if (url == null)
+ {
+ return null;
+ }
+ HttpURLConnection conn = null;
+ String protocol = url.getProtocol();
+ if ("http".equals(protocol) || "https".equals(protocol))
+ {
+ HttpURLConnection conn0 = (HttpURLConnection) url.openConnection();
+ if (conn0 != null)
+ {
+ conn = HttpUtils.followConnection(conn0);
+ }
+ else
+ {
+ conn = conn0;
+ }
+ }
+ return conn;
+ }
+
+ /**
+ * wrapper to follow a URL connection ALLOWING redirects from http to https
+ * and return the followed InputStream
+ *
+ * @param URL
+ * url
+ * @return HttpUrlConnection conn
+ */
+ public static InputStream openStream(URL url) throws IOException
+ {
+ if (url == null)
+ {
+ return null;
+ }
+ InputStream is = null;
+ String protocol = url.getProtocol();
+ if ("http".equals(protocol) || "https".equals(protocol))
+ {
+ HttpURLConnection conn = HttpUtils
+ .followConnection((HttpURLConnection) url.openConnection());
+ if (conn != null)
+ {
+ is = conn.getInputStream();
+ }
+ }
+ else
+ {
+ is = url.openStream();
+ }
+ return is;
+ }
+
+ /**
+ * check if a jalview:// scheme URL is given
+ *
+ * @param String
+ * uri
+ * @return boolean
+ */
+ public static boolean isJalviewSchemeUri(String jalviewUriString)
+ {
+ URI jalviewUri;
+ try
+ {
+ jalviewUri = new URI(jalviewUriString);
+ } catch (URISyntaxException e)
+ {
+ return false;
+ }
+ String scheme = jalviewUri.getScheme();
+ if (scheme == null || !scheme.startsWith("jalview"))
+ {
+ return false;
+ }
+ return scheme.length() == 7 // jalview
+ || scheme.length() == 8 // jalviewX
+ || scheme.substring(7).equals("http") // jalviewhttp
+ || scheme.substring(7).equals("https"); // jalviewhttps
+ }
+
+ /**
+ * convert a jalview scheme URI to its equivalent URL or path
+ *
+ * @param String
+ * uri
+ * @return String
+ */
+ public static String equivalentJalviewUrl(String jalviewUriString)
+ {
+ if (!isJalviewSchemeUri(jalviewUriString))
+ {
+ // not a jalviewUriString, hand it back
+ return jalviewUriString;
+ }
+ URI jalviewUri;
+ try
+ {
+ jalviewUri = new URI(jalviewUriString);
+ } catch (URISyntaxException e)
+ {
+ return null;
+ }
+ String scheme = jalviewUri.getScheme();
+ String host = jalviewUri.getHost();
+ if (host != null && host.length() > 0
+ || scheme.substring(7).startsWith("http"))
+ {
+ URI newUri;
+ try
+ {
+ newUri = new URI(scheme.equals("jalviewhttp") ? "http" : "https",
+ jalviewUri.getUserInfo(), host, jalviewUri.getPort(),
+ jalviewUri.getPath(), jalviewUri.getQuery(),
+ jalviewUri.getFragment());
+ // return a URL
+ return newUri.toURL().toString();
+ } catch (URISyntaxException | MalformedURLException e)
+ {
+ ErrorLog.errPrintln("Trying to convert '" + jalviewUriString
+ + "' to URL failed");
+ }
+ }
+ else
+ {
+ // return a file path (not a file URI)
+ return jalviewUri.getPath();
+ }
+ return null;
+ }
+}
public class LaunchUtils
{
-
// setting these is LaunchUtils so don't need to import Platform
public final static boolean isMac = System.getProperty("os.name")
.indexOf("Mac") > -1;
return null;
} catch (IOException e)
{
- System.err.println(e.getMessage());
+ ErrorLog.errPrintln(e.getMessage());
return null;
}
}
try
{
URL localFileURL = new URL(buildDetails);
- InputStream in = localFileURL.openStream();
+ InputStream in = HttpUtils.openStream(localFileURL);
Properties buildProperties = new Properties();
buildProperties.load(in);
in.close();
null);
if (JCV == null)
{
- System.out.println(
- "Could not obtain JAVA_COMPILE_VERSION for comparison");
+ ErrorLog.errPrintln("Could not obtain JAVA_COMPILE_VERSION for comparison");
return -2;
}
JAVA_COMPILE_VERSION = Integer.parseInt(JCV);
} catch (MalformedURLException e)
{
- System.err.println("Could not find " + buildDetails);
+ ErrorLog.errPrintln("Could not find " + buildDetails);
return -3;
} catch (IOException e)
{
- System.err.println("Could not load " + buildDetails);
+ ErrorLog.errPrintln("Could not load " + buildDetails);
return -4;
} catch (NumberFormatException e)
{
- System.err.println("Could not parse JAVA_COMPILE_VERSION");
+ ErrorLog.errPrintln("Could not parse JAVA_COMPILE_VERSION");
return -5;
}
String JV = System.getProperty("java.version");
if (JV == null)
{
- System.out.println("Could not obtain java.version for comparison");
+ ErrorLog.errPrintln("Could not obtain java.version for comparison");
return -2;
}
if (JV.startsWith("1."))
: Integer.parseInt(JV.substring(0, JV.indexOf(".")));
} catch (NumberFormatException e)
{
- System.err.println("Could not parse java.version");
+ ErrorLog.errPrintln("Could not parse java.version");
return -3;
}
return JAVA_VERSION;
if (java_compile_version <= 0 || java_version <= 0)
{
- System.out.println("Could not make Java version check");
+ ErrorLog.errPrintln("Could not make Java version check");
return true;
}
// Warn if these java.version and JAVA_COMPILE_VERSION conditions exist
jv.clear();
if (DEBUG)
{
- System.err.println("Array from '" + delimiter
+ ErrorLog.errPrintln("Array from '" + delimiter
+ "' separated List:\n" + v.length);
for (int i = 0; i < v.length; i++)
{
- System.err.println("item " + i + " '" + v[i] + "'");
+ ErrorLog.errPrintln("item " + i + " '" + v[i] + "'");
}
}
return v;
}
if (DEBUG)
{
- System.err.println(
+ ErrorLog.errPrintln(
"Empty Array from '" + delimiter + "' separated List");
}
return null;
{
System.err
.println("Returning '" + separator + "' separated List:\n");
- System.err.println(v);
+ ErrorLog.errPrintln(v.toString());
}
return v.toString();
}
if (DEBUG)
{
- System.err.println(
+ ErrorLog.errPrintln(
"Returning empty '" + separator + "' separated List\n");
}
return "" + separator;
return min < text.length() + 1 ? min : -1;
}
+ public static boolean equalsIgnoreCase(String s1, String s2)
+ {
+ if (s1 == null || s2 == null)
+ {
+ return s1 == s2;
+ }
+ return s1.toLowerCase(Locale.ROOT).equals(s2.toLowerCase(Locale.ROOT));
+ }
+
public static int indexOfFirstWhitespace(String text)
{
int index = -1;
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.3.1_FJVL</version>
+ <version>1.8.3-1.4.0_FJVL</version>
</parent>
<artifactId>getdown-launcher</artifactId>
BufferedReader reader = new BufferedReader(new InputStreamReader(in));
String line;
while ((line = reader.readLine()) != null) {
- out.print(line);
+ out.println(line);
out.flush();
}
} catch (IOException ioe) {
import com.threerings.getdown.util.StringUtil;
import static com.threerings.getdown.Log.log;
import jalview.bin.StartupNotificationListener;
+import jalview.util.HttpUtils;
/**
* The main application entry point for Getdown.
*/
public class GetdownApp
{
- public static String startupFilesParameterString = "";
+ public static List<String> startupFilesParameters = new ArrayList<>();
/**
* The main entry point of the Getdown launcher application.
*/
log.info("-- User Home: " + System.getProperty("user.home"));
log.info("-- Cur dir: " + System.getProperty("user.dir"));
log.info("-- Launcher version: "+Build.version());
- log.info("-- startupFilesParameterString: " + startupFilesParameterString);
+ log.info("-- startupFilesParameterString: " + getStartupFilesParameterString(getStartupFilesParameters(), false));
+ log.info("-- getStartupFilesParameterString(): " + getStartupFilesParameterString(getStartupFilesParameters(), true));
log.info("---------------------------------------------");
Getdown app = new Getdown(envc) {
protected JFrame _frame;
};
- String startupFile = getStartupFilesParameterString();
- if (!StringUtil.isBlank(startupFile)) {
- Application.setStartupFilesFromParameterString(startupFile);
+ if (getStartupFilesParameters().size() > 0) {
+ Application.setStartupFilesFromParameters(getStartupFilesParameters());
}
app.start();
return app;
}
- public static void setStartupFilesParameterString(String parameters) {
- startupFilesParameterString = parameters;
+ public static void addStartupFilesParameter(String parameter) {
+ startupFilesParameters.add(parameter);
}
- public static String getStartupFilesParameterString() {
- return startupFilesParameterString;
+ public static List<String> getStartupFilesParameters() {
+ return startupFilesParameters;
+ }
+
+ public static String getStartupFilesParameterString(List<String> parameters, boolean changeJalviewSchemeUris) {
+ StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for(String f : parameters) {
+ if (first) {
+ first = false;
+ } else {
+ sb.append(' ');
+ }
+ String p = changeJalviewSchemeUris ? HttpUtils.equivalentJalviewUrl(f) : f;
+ if (p.contains(" ")) {
+ sb.append('"');
+ sb.append(p);
+ sb.append('"');
+ } else {
+ sb.append(p);
+ }
+ }
+ return sb.toString();
}
}
com.install4j.api.launcher.StartupNotification.registerStartupListener(
new com.install4j.api.launcher.StartupNotification.Listener() {
@Override
- public void startupPerformed(String parameters) {
- log.info("StartupNotification.Listener.startupPerformed: '"+parameters+"'");
- GetdownApp.setStartupFilesParameterString(parameters);
+ public void startupPerformed(String parameter) {
+ log.info("StartupNotification.Listener.startupPerformed: '"+parameter+"'");
+ GetdownApp.addStartupFilesParameter(parameter);
}
}
);
if [ x$JVLVERSION != x ]; then
export VERSION=$JVLVERSION
else
- export VERSION=1.8.3-1.3.1_JVL
+ export VERSION=1.8.3-1.4.0_JVL
fi
if [ x${VERSION%_JVL} = x$VERSION ]; then
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
<packaging>pom</packaging>
- <version>1.8.3-1.3.1_FJVL</version>
+ <version>1.8.3-1.4.0_FJVL</version>
<name>getdown</name>
<description>An application installer and updater.</description>
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
-import java.net.URLConnection;
import java.net.URLEncoder;
import java.nio.charset.StandardCharsets;
import java.util.AbstractMap;
import jalview.bin.Console;
import jalview.util.ChannelProperties;
import jalview.util.HttpUtils;
+import jalview.util.UserAgent;
public class Plausible
{
// random clientId to make User-Agent unique (to register analytic)
clientId = String.format("%08x", new Random().nextInt());
- USER_AGENT = HttpUtils.getUserAgent(
+ USER_AGENT = UserAgent.getUserAgent(
MethodHandles.lookup().lookupClass().getCanonicalName() + " "
+ clientId);
}
try
{
URL url = new URL(urlSb.toString());
- URLConnection urlConnection = url.openConnection();
- HttpURLConnection httpURLConnection = (HttpURLConnection) urlConnection;
+ HttpURLConnection httpURLConnection = HttpUtils.openConnection(url);
httpURLConnection.setRequestMethod("POST");
httpURLConnection.setDoOutput(true);
try
{
URL url = new URL(CONFIG_API_BASE_URL);
- URLConnection urlConnection = url.openConnection();
- HttpURLConnection httpURLConnection = (HttpURLConnection) urlConnection;
+ HttpURLConnection httpURLConnection = HttpUtils.openConnection(url);
httpURLConnection.setRequestMethod("GET");
httpURLConnection.setRequestProperty("User-Agent", USER_AGENT);
httpURLConnection.setConnectTimeout(5000);
import jalview.urls.IdOrgSettings;
import jalview.util.ChannelProperties;
import jalview.util.ColorUtils;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
try
{
// props file provided as URL
- fis = new URL(propertiesFile).openStream();
+ fis = HttpUtils.openStream(new URL(propertiesFile));
if (!Jalview.quiet())
{
jalview.bin.Console.outPrintln(
URL url = new URL(remoteBuildPropertiesUrl);
BufferedReader in = new BufferedReader(
- new InputStreamReader(url.openStream()));
+ new InputStreamReader(HttpUtils.openStream(url)));
Properties remoteBuildProperties = new Properties();
remoteBuildProperties.load(in);
if (customProxySet &&
// we have a username but no password for the scheme being
// requested
- (protocol.equalsIgnoreCase("http")
- && (httpUser != null && httpUser.length() > 0
- && (httpPassword == null
- || httpPassword.length == 0)))
+ (protocol.equalsIgnoreCase("http")
+ && (httpUser != null
+ && httpUser.length() > 0
+ && (httpPassword == null
+ || httpPassword.length == 0)))
|| (protocol.equalsIgnoreCase("https")
&& (httpsUser != null
&& httpsUser.length() > 0
import java.awt.Color;
import java.io.File;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.ArrayList;
{
Arg a = av.getArg();
SubVals sv = av.getSubVals();
- String openFile = av.getValue();
+ String openFile0 = av.getValue();
+ String openFile = HttpUtils.equivalentJalviewUrl(openFile0);
if (openFile == null)
continue;
try
{
format = new IdentifyFile().identify(openFile, protocol);
+ } catch (FileNotFoundException e0)
+ {
+ addError((protocol == DataSourceType.URL ? "File at URL" : "File")
+ + " '" + openFile + "' not found");
} catch (FileFormatException e1)
{
addError("Unknown file format for '" + openFile + "'");
{
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
+ if (!openFile.equals(openFile0))
+ {
+ af.setTitle(openFile0);
+ }
} catch (Throwable thr)
{
xception = true;
private void colourAlignFrame(AlignFrame af, ColourSchemeI cs)
{
- try {
- SwingUtilities.invokeAndWait(new Runnable()
+ try
{
- @Override
- public void run()
+ SwingUtilities.invokeAndWait(new Runnable()
{
- // Note that cs == null removes colour scheme from af
- af.changeColour(cs);
- }
- }); } catch (Exception x) {
- Console.trace("Interrupted whilst waiting for colorAlignFrame action",x);
-
+ @Override
+ public void run()
+ {
+ // Note that cs == null removes colour scheme from af
+ af.changeColour(cs);
+ }
+ });
+ } catch (Exception x)
+ {
+ Console.trace("Interrupted whilst waiting for colorAlignFrame action",
+ x);
+
}
}
import java.lang.management.ManagementFactory;
import java.lang.management.OperatingSystemMXBean;
+import jalview.util.ErrorLog;
+
/**
* Isolated class to ascertain physical memory of the system using
* com.sun.management.OperatingSystemMXBean class's getTotalPhysicalMemorySize
} catch (NoClassDefFoundError e)
{
// com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
- jalview.bin.Console.errPrintln(
+ ErrorLog.errPrintln(
"No com.sun.management.OperatingSystemMXBean: cannot get total physical memory size");
}
import java.awt.HeadlessException;
import java.util.Locale;
+import jalview.util.ErrorLog;
+
public class HiDPISetting
{
private static final int hidpiThreshold = 160;
}
} catch (NumberFormatException e)
{
- jalview.bin.Console.errPrintln(setHiDPIScalePropertyName
- + " property give (" + setHiDPIScaleProperty
- + ") but not parseable as integer");
+ ErrorLog.errPrintln(setHiDPIScalePropertyName + " property give ("
+ + setHiDPIScaleProperty + ") but not parseable as integer");
}
}
if (setHiDPI && setHiDPIScale > 0)
try
{
int existingPropertyVal = Integer.parseInt(existingProperty);
- jalview.bin.Console.outPrintln("Existing " + scalePropertyName
- + " is " + existingPropertyVal);
+ ErrorLog.outPrintln("Existing " + scalePropertyName + " is "
+ + existingPropertyVal);
if (existingPropertyVal > 1)
{
setHiDPIScale(existingPropertyVal);
}
} catch (NumberFormatException e)
{
- jalview.bin.Console.outPrintln(
+ ErrorLog.outPrintln(
"Could not convert property " + scalePropertyName
+ " vale '" + existingProperty + "' to number");
}
{
if (isLinux)
{
- jalview.bin.Console.errPrintln(
+ ErrorLog.errPrintln(
"Cannot get screen resolution: " + e.getMessage());
}
}
{
if (isLinux)
{
- jalview.bin.Console
- .errPrintln("Cannot get screen size height and width:"
- + e.getMessage());
+ ErrorLog.errPrintln("Cannot get screen size height and width:"
+ + e.getMessage());
}
}
import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
+import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import jalview.util.LaunchUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.UserAgent;
import jalview.ws.jws2.Jws2Discoverer;
/**
{
headless = true;
}
- System.setProperty("http.agent", HttpUtils.getUserAgent());
+ System.setProperty("http.agent", UserAgent.getUserAgent());
try
{
try
{
format = new IdentifyFile().identify(file, protocol);
- } catch (FileFormatException e1)
+ } catch (FileNotFoundException e)
{
- // TODO ?
+ Console.error("File at '" + file + "' not found", e);
+ } catch (FileFormatException e)
+ {
+ Console.error("File '" + file + "' format not recognised", e);
}
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
try
{
format = new IdentifyFile().identify(file, protocol);
+ } catch (FileNotFoundException e)
+ {
+ Console.error("File at '" + file + "' not found", e);
} catch (FileFormatException e)
{
- // TODO what?
+ Console.error("File '" + file + "' format not recognised", e);
}
}
*/
package jalview.bin;
+import java.applet.Applet;
+import java.awt.Button;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.EventQueue;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
import java.util.Locale;
+import java.util.StringTokenizer;
+import java.util.Vector;
import jalview.analysis.AlignmentUtils;
import jalview.api.StructureSelectionManagerProvider;
import jalview.util.ColorUtils;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
-
-import java.applet.Applet;
-import java.awt.Button;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.EventQueue;
-import java.awt.Font;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.event.ActionEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
import netscape.javascript.JSObject;
/**
try
{
BufferedReader reader = new BufferedReader(
- new InputStreamReader(url.openStream()));
+ new InputStreamReader(HttpUtils.openStream(url)));
String line;
while ((line = reader.readLine()) != null)
{
PDBEntry[] pdb = new PDBEntry[pdbs.size()];
String[][] chains = new String[pdbs.size()][];
String[] protocols = new String[pdbs.size()];
- for (int pdbsi = 0, pdbsiSize = pdbs
- .size(); pdbsi < pdbsiSize; pdbsi++)
+ for (int pdbsi = 0,
+ pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
{
Object[] o = (Object[]) pdbs.elementAt(pdbsi);
pdb[pdbsi] = (PDBEntry) o[0];
import java.util.Locale;
-import jalview.bin.argparser.Arg;
+import jalview.util.ErrorLog;
/**
* Methods to decide on appropriate memory setting for Jalview based on two
*/
public class MemorySetting
{
- public static final String MAX_HEAPSIZE_PERCENT_PROPERTY_NAME = Arg.JVMMEMPC
- .getName();
+ // This must match the value of Arg.JVMMEMPC.getName()
+ public static final String MAX_HEAPSIZE_PERCENT_PROPERTY_NAME = "jvmmempc";
- public static final String MAX_HEAPSIZE_PROPERTY_NAME = Arg.JVMMEMMAX
- .getName();
+ // This must match the value of Arg.JVMMEMMAX.getName()
+ public static final String MAX_HEAPSIZE_PROPERTY_NAME = "jvmmemmax";
private static final int MAX_HEAPSIZE_PERCENT_DEFAULT = 90; // 90%
else
{
// number too big for a Long. Limit to Long.MAX_VALUE
- jalview.bin.Console.outPrintln("Memory parsing of '" + memString
+ ErrorLog.outPrintln("Memory parsing of '" + memString
+ "' produces number too big. Limiting to Long.MAX_VALUE="
+ Long.MAX_VALUE);
return Long.MAX_VALUE;
ADJUSTMENT_MESSAGE = reason;
if (!quiet)
{
- jalview.bin.Console.outPrintln(reason);
+ ErrorLog.outPrintln(reason);
}
}
import java.util.List;
import java.util.Map;
+import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.bin.Jalview.ExitCode;
import jalview.bin.argparser.Arg.Opt;
import jalview.bin.argparser.Arg.Type;
+import jalview.util.ArgParserUtils;
import jalview.util.FileUtils;
import jalview.util.HttpUtils;
return;
}
+ // preprocess for associated files only if no actual --args supplied
+ Console.debug("Supplied args are " + args);
+ if (!dd && !Cache.getDefault("NOARGPREPROCESSING", false))
+ {
+ ArgParserUtils.preProcessArgs(args);
+ Console.debug("Preprocessed args are " + args);
+ }
+
if (bsa != null)
{
this.bootstrapArgs = bsa;
import org.json.simple.parser.ParseException;
+import jalview.util.HttpUtils;
import jalview.util.Platform;
import jalview.util.StringUtils;
{
// jalview.bin.Console.outPrintln(System.currentTimeMillis() + " " + url);
- HttpURLConnection connection = (HttpURLConnection) url.openConnection();
+ HttpURLConnection connection = HttpUtils.openConnection(url);
/*
* POST method allows multiple queries in one request; it is supported for
import org.json.simple.parser.ContentHandler;
import org.json.simple.parser.ParseException;
+import jalview.util.HttpUtils;
import jalview.util.JSONUtils;
import jalview.util.MessageManager;
import jalview.ws.HttpClientUtils;
// return processJsonResponseFor(new
// InputStreamReader(geturl.openStream()));
ArrayList<Reader> readers = new ArrayList<>();
- readers.add(new InputStreamReader(geturl.openStream()));
+ readers.add(new InputStreamReader(HttpUtils.openStream(geturl)));
return readers.iterator();
}
import jalview.bin.Console;
import jalview.gui.Preferences;
import jalview.structure.StructureCommandI;
+import jalview.util.HttpUtils;
import jalview.util.Platform;
public class PymolManager
try
{
URL realUrl = new URL(rpcUrl);
- HttpURLConnection conn = (HttpURLConnection) realUrl.openConnection();
+ HttpURLConnection conn = HttpUtils.openConnection(realUrl);
conn.setRequestProperty("accept", "*/*");
conn.setRequestProperty("content-type", "text/xml");
conn.setDoOutput(true);
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
+import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
try
{
format = new IdentifyFile().identify(text, DataSourceType.PASTE);
+ } catch (FileNotFoundException e0)
+ {
+ // this won't happen
} catch (FileFormatException e1)
{
// leave as null
import java.beans.PropertyChangeListener;
import java.beans.PropertyVetoException;
import java.io.File;
+import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.lang.reflect.Field;
try
{
format = new IdentifyFile().identify(url, DataSourceType.URL);
+ } catch (FileNotFoundException e)
+ {
+ jalview.bin.Console.error("URL '" + url + "' not found", e);
} catch (FileFormatException e)
{
- // TODO revise error handling, distinguish between
- // URL not found and response not valid
+ jalview.bin.Console.error(
+ "File at URL '" + url + "' format not recognised", e);
}
if (format == null)
if (alignViewport.getWrapAlignment())
{
drawIdsWrapped(g, alignViewport, startSeq, getHeight(),
- manuallyAdjusted ? panelWidth : -1, forGUI);
+ isManuallyAdjusted() ? panelWidth : -1, forGUI);
return;
}
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.bin.Console;
-import jalview.util.MessageManager;
-
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.net.URL;
-import javax.swing.JOptionPane;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
public class UserQuestionnaireCheck implements Runnable
{
// see if we have already responsed to this questionnaire or get a new
// qid/rid pair
BufferedReader br = new BufferedReader(
- new InputStreamReader(qurl.openStream()));
+ new InputStreamReader(HttpUtils.openStream(qurl)));
String qresp;
while ((qresp = br.readLine()) != null)
{
import jalview.gui.OOMWarning;
import jalview.json.binding.biojs.BioJSReleasePojo;
import jalview.json.binding.biojs.BioJSRepositoryPojo;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
public class BioJsHTMLOutput extends HTMLOutput
try
{
URL resourceUrl = new URL(url);
- is = new BufferedInputStream(resourceUrl.openStream());
+ is = new BufferedInputStream(HttpUtils.openStream(resourceUrl));
BufferedReader br = new BufferedReader(new InputStreamReader(is));
responseStrBuilder = new StringBuilder();
String lineContent;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
+import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
+import java.net.UnknownHostException;
import java.util.zip.GZIPInputStream;
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Console;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
{
errormessage = "URL NOT FOUND";
URL url = new URL(urlStr);
- URLConnection _conn = url.openConnection();
+ URLConnection _conn = HttpUtils.openConnection(url);
if (_conn instanceof HttpURLConnection)
{
- HttpURLConnection conn = (HttpURLConnection) _conn;
+ HttpURLConnection conn = HttpUtils
+ .followConnection((HttpURLConnection) _conn);
int rc = conn.getResponseCode();
if (rc != HttpURLConnection.HTTP_OK)
{
- throw new IOException(
- "Response status from " + urlStr + " was " + rc);
+ throw new FileNotFoundException("Response status from " + urlStr
+ + " was " + conn.getResponseCode());
}
+ _conn = conn;
}
else
{
* @throws IOException
*/
public FileParse(Object file, DataSourceType sourceType)
- throws MalformedURLException, IOException
+ throws MalformedURLException, FileNotFoundException, IOException
{
if (file instanceof File)
{
}
private void parse(File file, String fileStr, DataSourceType sourceType,
- boolean isFileObject) throws IOException
+ boolean isFileObject) throws FileNotFoundException, IOException
{
bytes = Platform.getFileBytes(file);
dataSourceType = sourceType;
error = false;
+ boolean filenotfound = false;
if (sourceType == DataSourceType.FILE)
{
String suffixLess = extractSuffix(fileStr);
if (suffixLess == null)
{
+ if (e instanceof FileNotFoundException
+ || e instanceof UnknownHostException)
+ {
+ errormessage = "File at URL '" + fileStr + "' not found";
+ filenotfound = true;
+ }
throw (e);
}
else
checkURLSource(suffixLess);
} catch (IOException e2)
{
- errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
+ errormessage = "BAD URL WITH OR WITHOUT SUFFIX '" + fileStr
+ + "'";
+ if (e instanceof FileNotFoundException)
+ {
+ filenotfound = true;
+ }
throw (e); // just pass back original - everything was wrong.
}
}
if (dataIn == null || error)
{
// pass up the reason why we have no source to read from
+ if (filenotfound)
+ {
+ throw new FileNotFoundException(MessageManager
+ .formatMessage("label.url_not_found", new String[]
+ { errormessage }));
+ }
throw new IOException(MessageManager.formatMessage(
"exception.failed_to_read_data_from_source", new String[]
{ errormessage }));
return new BufferedReader(new FileReader((File) file));
case URL:
URL url = new URL(file.toString());
- in = new BufferedReader(new InputStreamReader(url.openStream()));
+ in = new BufferedReader(
+ new InputStreamReader(HttpUtils.openStream(url)));
break;
case RELATIVE_URL: // JalviewJS only
bytes = Platform.getFileAsBytes(file.toString());
import jalview.gui.AlignmentPanel;
import jalview.gui.IProgressIndicator;
import jalview.io.exceptions.ImageOutputException;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
public abstract class HTMLOutput implements Runnable
{
try
{
- isReader = new InputStreamReader(url.openStream());
+ isReader = new InputStreamReader(HttpUtils.openStream(url));
buffReader = new BufferedReader(isReader);
String line;
String lineSeparator = System.getProperty("line.separator");
package jalview.io;
import java.io.File;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Locale;
private static final String XMLHEADER = "<?XML VERSION=\"1.0\" ENCODING=\"UTF-8\" STANDALONE=\"YES\"?>";
public FileFormatI identify(Object file, DataSourceType protocol)
- throws FileFormatException
+ throws FileFormatException, FileNotFoundException
{
// BH 2018
return (file instanceof File ? identify((File) file, protocol)
* @throws FileFormatException
*/
public FileFormatI identify(String file, DataSourceType sourceType)
- throws FileFormatException
+ throws FileFormatException, FileNotFoundException
{
String emessage = "UNIDENTIFIED FILE PARSING ERROR";
FileParse parser = null;
+ FileNotFoundException fnf = null;
try
{
parser = new FileParse(file, sourceType);
{
return identify(parser);
}
+ } catch (FileNotFoundException e)
+ {
+ fnf = e;
+ emessage = "Could not find '" + file + "'";
+ Console.error("Could not find '" + file + "'", e);
+ } catch (IOException e)
+ {
+ Console.error("Error whilst trying to read " + file, e);
} catch (Exception e)
{
Console.error("Error whilst identifying " + file, e);
{
throw new FileFormatException(parser.errormessage);
}
+ if (fnf != null)
+ {
+ throw (fnf);
+ }
throw new FileFormatException(emessage);
}
try
{
type = ider.identify(args[i], DataSourceType.FILE);
+ } catch (FileNotFoundException e)
+ {
+ Console.error(String.format("Error '%s' fetching file %s", args[i],
+ e.getMessage()));
} catch (FileFormatException e)
{
Console.error(
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactMatrix;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
import jalview.datamodel.GroupSet;
-import jalview.datamodel.GroupSetI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
// jalview.bin.Console.outPrintln("Jalview2XML: opening url
// jarInputStream for "
// + _url);
- return new JarInputStream(_url.openStream());
+ return new JarInputStream(HttpUtils.openStream(_url));
}
else
{
--- /dev/null
+package jalview.util;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Set;
+
+import jalview.bin.Cache;
+import jalview.bin.argparser.Arg;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+
+public class ArgParserUtils
+{
+ private static Set<String> alignmentExtensions = null;
+
+ private static Set<String> annotationsExtensions = null;
+
+ private static Set<String> featuresExtensions = null;
+
+ private static Set<String> treeExtensions = null;
+
+ public static void preProcessArgs(List<String> filenames)
+ {
+ // Running through the arguments to look for '-arg' or '--arg' should
+ // already have happened, not doing it again.
+ if (alignmentExtensions == null)
+ {
+ setValidExtensions();
+ }
+
+ Set<String> filesSet = new HashSet<>(filenames);
+
+ List<Arg> argSet = new ArrayList<>();
+ argSet.add(Arg.ANNOTATIONS);
+ argSet.add(Arg.FEATURES);
+ argSet.add(Arg.TREE);
+
+ Map<Arg, Set<String>> argExtensionsMap = new HashMap<>();
+ argExtensionsMap.put(Arg.ANNOTATIONS, annotationsExtensions);
+ argExtensionsMap.put(Arg.FEATURES, featuresExtensions);
+ argExtensionsMap.put(Arg.TREE, treeExtensions);
+
+ Map<String, BaseInfo> baseInfoMap = new HashMap<>();
+
+ // we make a copy to run through, and delete associated filenames from the
+ // original
+ final List<String> filenamesCopy = new ArrayList<>(filenames);
+ for (String filename : filenamesCopy)
+ {
+ if (filename == null)
+ {
+ continue;
+ }
+ String ext = FileUtils.getExtension(filename);
+ if (ext != null && ext.length() > 0
+ && alignmentExtensions.contains(ext))
+ {
+ BaseInfo bi = new BaseInfo(filename);
+
+ // this includes the dot at the end of the basename
+ String base = FileUtils.getBase(filename);
+
+ for (Arg arg : argSet)
+ {
+ for (String possibleExt : argExtensionsMap.get(arg))
+ {
+ String possibleFile = base + possibleExt;
+ if (filesSet.contains(possibleFile))
+ {
+ bi.putAssociatedFile(arg, possibleFile);
+ filenames.remove(possibleFile);
+ break;
+ }
+ }
+ }
+
+ baseInfoMap.put(filename, bi);
+ }
+ }
+
+ // now we go through the saved associated files and add them back in to the
+ // right places with the appropriate argument
+ for (String filename : baseInfoMap.keySet())
+ {
+ BaseInfo bi = baseInfoMap.get(filename);
+
+ int pos = filenames.indexOf(filename);
+ if (bi.associatedFiles != null)
+ {
+ for (Arg a : bi.associatedFiles.keySet())
+ {
+ String associatedFile = bi.associatedFiles.get(a);
+ if (associatedFile == null)
+ {
+ // shouldn't happen!
+ continue;
+ }
+ filenames.add(pos + 1, a.argString());
+ filenames.add(pos + 2,
+ HttpUtils.equivalentJalviewUrl(associatedFile));
+ }
+ }
+ // add an --open arg to separate from other files
+ filenames.add(pos, Arg.OPEN.argString());
+ }
+ }
+
+ private static void setValidExtensions()
+ {
+ alignmentExtensions = new HashSet<>();
+ FileFormats ffs = FileFormats.getInstance();
+ List<String> validFormats = ffs.getReadableFormats();
+
+ for (String fname : validFormats)
+ {
+ FileFormatI tff = ffs.forName(fname);
+ String[] extensions = tff.getExtensions().split(",");
+ for (String ext : extensions)
+ {
+ alignmentExtensions.add(ext.toLowerCase(Locale.ROOT));
+ }
+ }
+
+ annotationsExtensions = new HashSet<>();
+ for (String ext : Cache
+ .getDefault("ARGPREPROCESSORANNOTATIONSEXTENSIONS",
+ "annotation,annotations")
+ .split(","))
+ {
+ annotationsExtensions.add(ext);
+ }
+
+ featuresExtensions = new HashSet<>();
+ for (String ext : Cache.getDefault("ARGPREPROCESSORFEATURESEXTENSIONS",
+ "feature,features").split(","))
+ {
+ featuresExtensions.add(ext);
+ }
+
+ treeExtensions = new HashSet<>();
+ for (String ext : Cache.getDefault("ARGPREPROCESSORTREEEXTENSIONS",
+ "tree,tre,newick,nwk").split(","))
+ {
+ treeExtensions.add(ext);
+ }
+ }
+}
+
+class BaseInfo
+{
+ String filename;
+
+ Map<Arg, String> associatedFiles = null;
+
+ BaseInfo(String filename)
+ {
+ this.filename = filename;
+ }
+
+ void putAssociatedFile(Arg a, String file)
+ {
+ if (associatedFiles == null)
+ {
+ associatedFiles = new HashMap<>();
+ }
+ associatedFiles.put(a, file);
+ }
+}
if (channelPropsURL == null)
{
// complete failure of channel_properties, set all properties to defaults
- jalview.bin.Console.errPrintln("Failed to find '/"
- + CHANNEL_PROPERTIES_FILENAME + "' file at '"
+ ErrorLog.errPrintln("Failed to find '/" + CHANNEL_PROPERTIES_FILENAME
+ + "' file at '"
+ (channelPropsURL == null ? "null"
: channelPropsURL.toString())
+ "'. Using class defaultProps.");
{
try
{
- InputStream channelPropsIS = channelPropsURL.openStream();
+ InputStream channelPropsIS = HttpUtils.openStream(channelPropsURL);
tryChannelProps.load(channelPropsIS);
channelPropsIS.close();
} catch (IOException e)
{
- jalview.bin.Console.errPrintln(e.getMessage());
+ ErrorLog.errPrintln(e.getMessage());
// return false;
}
}
channelProps.load(is);
} catch (FileNotFoundException e)
{
- jalview.bin.Console.errPrintln(e.getMessage());
+ ErrorLog.errPrintln(e.getMessage());
} catch (IOException e)
{
- jalview.bin.Console.errPrintln(e.getMessage());
+ ErrorLog.errPrintln(e.getMessage());
}
}
}
}
else
{
- jalview.bin.Console
- .errPrintln("Failed to get channel property '" + key + "'");
+ ErrorLog.errPrintln("Failed to get channel property '" + key + "'");
}
}
return null;
img = imgIcon == null ? null : imgIcon.getImage();
if (img == null)
{
- jalview.bin.Console.errPrintln(
+ ErrorLog.errPrintln(
"Failed to load channel image " + key + "=" + path);
if (!useClassDefaultImage)
{
{
return urlMap().getOrDefault(key, null);
}
- jalview.bin.Console.errPrintln(
+ ErrorLog.errPrintln(
"Do not use getImageURL(key) before using getImage(key...)");
}
return null;
--- /dev/null
+package jalview.util;
+
+public class ErrorLog
+{
+ private static boolean hasConsole = true;
+
+ public static void outPrintln(String message)
+ {
+ println(message, false);
+ }
+
+ public static void errPrintln(String message)
+ {
+ println(message, true);
+ }
+
+ public static void println(String message, boolean err)
+ {
+ if (hasConsole)
+ {
+ try
+ {
+ hasConsole = jalview.bin.Console.initLogger();
+ if (hasConsole)
+ {
+ if (err)
+ {
+ jalview.bin.Console.errPrintln(message);
+ }
+ else
+ {
+ jalview.bin.Console.outPrintln(message);
+ }
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ } catch (NoClassDefFoundError t)
+ {
+ hasConsole = false;
+ System.err.println(
+ "jalview.util.ErrorLog has no jalview.bin.Console. Using System.err and System.out.");
+ }
+ }
+ if (!hasConsole)
+ {
+ if (err)
+ {
+ System.err.println("jalview.util.ErrorLog: " + message);
+ }
+ else
+ {
+ System.out.println("jalview.util.ErrorLog: " + message);
+
+ }
+ }
+ }
+}
import java.io.File;
import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.nio.file.FileSystems;
import java.nio.file.FileVisitOption;
import java.nio.file.FileVisitResult;
return parentDir.mkdirs();
}
+
+ /**
+ * get a guessed file extension from a String only
+ *
+ * @param String
+ * filename
+ * @return String extension
+ */
+ public static String getExtension(String filename)
+ {
+ return getBaseOrExtension(filename, true);
+ }
+
+ /**
+ * getBase returns everything in a path/URI up to (and including) an extension
+ * dot. Note this is not the same as getBasename() since getBasename() only
+ * gives the filename base, not the path too. If no extension dot is found
+ * (i.e. a dot in character position 2 or more of the filename (after the last
+ * slash) then the whole path is considered the base.
+ *
+ * @param filename
+ * @return String base
+ */
+ public static String getBase(String filename)
+ {
+ return getBaseOrExtension(filename, false);
+ }
+
+ public static String getBaseOrExtension(String filename0,
+ boolean extension)
+ {
+ if (filename0 == null)
+ {
+ return null;
+ }
+ String filename = filename0;
+ boolean isUrl = false;
+ if (HttpUtils.startsWithHttpOrHttps(filename))
+ {
+ try
+ {
+ URL url = new URL(filename);
+ filename = url.getPath();
+ isUrl = true;
+ } catch (MalformedURLException e)
+ {
+ // continue to treat as a filename
+ }
+ }
+ int dot = filename.lastIndexOf('.');
+ int slash = filename.lastIndexOf('/');
+ if (!File.separator.equals("/") && !isUrl)
+ {
+ slash = filename.lastIndexOf(File.separator);
+ }
+ // only the dot of the filename (not dots in path) and not if it's a .hidden
+ // file
+ boolean hasExtension = dot > slash + 1;
+ if (extension)
+ {
+ return hasExtension ? filename.substring(dot + 1) : null;
+ }
+ else
+ {
+ dot = filename0.lastIndexOf('.');
+ return hasExtension ? filename0.substring(0, dot + 1) : filename0;
+ }
+ }
}
import java.io.IOException;
import java.io.InputStream;
import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
import java.net.ProtocolException;
+import java.net.URI;
+import java.net.URISyntaxException;
import java.net.URL;
-import javax.ws.rs.HttpMethod;
-
-import jalview.bin.Cache;
-
public class HttpUtils
{
InputStream is = null;
try
{
- is = new URL(url).openStream();
+ is = HttpUtils.openStream(new URL(url));
if (is != null)
{
return true;
// jalview.bin.Console.outPrintln(System.currentTimeMillis() + " " + url);
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
-
- connection.setRequestMethod(HttpMethod.HEAD);
-
+ connection.setRequestMethod("HEAD");
connection.setDoInput(true);
-
connection.setUseCaches(false);
connection.setConnectTimeout(300);
connection.setReadTimeout(readTimeout);
- return connection.getResponseCode() == 200;
+
+ // HttpURLConnection doesn't follow redirects from http to https. It should!
+ HttpURLConnection conn = followConnection(connection);
+ return conn.getResponseCode() == 200;
+ }
+
+ /**
+ * wrapper to follow a URL connection ALLOWING redirects from http to https
+ *
+ * @param HttpURLConnection
+ * conn0
+ * @return HttpUrlConnection conn
+ */
+ public static HttpURLConnection followConnection(HttpURLConnection conn0)
+ throws IOException
+ {
+ URL url = conn0.getURL();
+ if (url == null)
+ {
+ return null;
+ }
+ HttpURLConnection conn = null;
+ int response = conn0.getResponseCode();
+ boolean followed = false;
+ if (response >= 300 && response < 400 && conn0.getFollowRedirects())
+ {
+ // we are only checking for a redirect from http to https
+ if ("http".equals(url.getProtocol()))
+ {
+ URL loc = new URL(conn0.getHeaderField("Location"));
+ if (loc != null && "https".equals(loc.getProtocol()))
+ {
+ conn = (HttpURLConnection) loc.openConnection();
+ conn.setRequestMethod(conn0.getRequestMethod());
+ conn.setDoInput(conn0.getDoInput());
+ conn.setUseCaches(conn0.getUseCaches());
+ conn.setConnectTimeout(conn0.getConnectTimeout());
+ conn.setReadTimeout(conn0.getReadTimeout());
+ conn.setInstanceFollowRedirects(
+ conn0.getInstanceFollowRedirects());
+ followed = true;
+ }
+ }
+ }
+ return followed && conn != null ? conn : conn0;
+ }
+
+ /**
+ * wrapper to follow a URL connection ALLOWING redirects from http to https
+ *
+ * @param URL
+ * url
+ * @return HttpUrlConnection conn
+ */
+ public static HttpURLConnection openConnection(URL url) throws IOException
+ {
+ if (url == null)
+ {
+ return null;
+ }
+ HttpURLConnection conn = null;
+ String protocol = url.getProtocol();
+ if ("http".equals(protocol) || "https".equals(protocol))
+ {
+ HttpURLConnection conn0 = (HttpURLConnection) url.openConnection();
+ if (conn0 != null)
+ {
+ conn = HttpUtils.followConnection(conn0);
+ }
+ else
+ {
+ conn = conn0;
+ }
+ }
+ return conn;
}
- public static String getUserAgent()
+ /**
+ * wrapper to follow a URL connection ALLOWING redirects from http to https
+ * and return the followed InputStream
+ *
+ * @param URL
+ * url
+ * @return HttpUrlConnection conn
+ */
+ public static InputStream openStream(URL url) throws IOException
{
- return getUserAgent(null);
+ if (url == null)
+ {
+ return null;
+ }
+ InputStream is = null;
+ String protocol = url.getProtocol();
+ if ("http".equals(protocol) || "https".equals(protocol))
+ {
+ HttpURLConnection conn = HttpUtils
+ .followConnection((HttpURLConnection) url.openConnection());
+ if (conn != null)
+ {
+ is = conn.getInputStream();
+ }
+ }
+ else
+ {
+ is = url.openStream();
+ }
+ return is;
}
- public static String getUserAgent(String className)
+ /**
+ * check if a jalview:// scheme URL is given
+ *
+ * @param String
+ * uri
+ * @return boolean
+ */
+ public static boolean isJalviewSchemeUri(String jalviewUriString)
{
- StringBuilder sb = new StringBuilder();
- sb.append("Jalview");
- sb.append('/');
- sb.append(Cache.getDefault("VERSION", "Unknown"));
- sb.append(" (");
- sb.append(System.getProperty("os.name"));
- sb.append("; ");
- sb.append(System.getProperty("os.arch"));
- sb.append(' ');
- sb.append(System.getProperty("os.name"));
- sb.append(' ');
- sb.append(System.getProperty("os.version"));
- sb.append("; ");
- sb.append("java/");
- sb.append(System.getProperty("java.version"));
- sb.append("; ");
- sb.append("jalview/");
- sb.append(ChannelProperties.getProperty("channel"));
- if (className != null)
- {
- sb.append("; ");
- sb.append(className);
+ URI jalviewUri;
+ try
+ {
+ jalviewUri = new URI(jalviewUriString);
+ } catch (URISyntaxException e)
+ {
+ return false;
}
- String installation = Cache.applicationProperties
- .getProperty("INSTALLATION");
- if (installation != null)
+ String scheme = jalviewUri.getScheme();
+ if (scheme == null || !scheme.startsWith("jalview"))
{
- sb.append("; ");
- sb.append(installation);
+ return false;
}
- sb.append(')');
- sb.append(" help@jalview.org");
- return sb.toString();
+ return scheme.length() == 7 // jalview
+ || scheme.length() == 8 // jalviewX
+ || scheme.substring(7).equals("http") // jalviewhttp
+ || scheme.substring(7).equals("https"); // jalviewhttps
}
+ /**
+ * convert a jalview scheme URI to its equivalent URL or path
+ *
+ * @param String
+ * uri
+ * @return String
+ */
+ public static String equivalentJalviewUrl(String jalviewUriString)
+ {
+ if (!isJalviewSchemeUri(jalviewUriString))
+ {
+ // not a jalviewUriString, hand it back
+ return jalviewUriString;
+ }
+ URI jalviewUri;
+ try
+ {
+ jalviewUri = new URI(jalviewUriString);
+ } catch (URISyntaxException e)
+ {
+ return null;
+ }
+ String scheme = jalviewUri.getScheme();
+ String host = jalviewUri.getHost();
+ if (host != null && host.length() > 0
+ || scheme.substring(7).startsWith("http"))
+ {
+ URI newUri;
+ try
+ {
+ newUri = new URI(scheme.equals("jalviewhttp") ? "http" : "https",
+ jalviewUri.getUserInfo(), host, jalviewUri.getPort(),
+ jalviewUri.getPath(), jalviewUri.getQuery(),
+ jalviewUri.getFragment());
+ // return a URL
+ return newUri.toURL().toString();
+ } catch (URISyntaxException | MalformedURLException e)
+ {
+ ErrorLog.errPrintln("Trying to convert '" + jalviewUriString
+ + "' to URL failed");
+ }
+ }
+ else
+ {
+ // return a file path (not a file URI)
+ return jalviewUri.getPath();
+ }
+ return null;
+ }
}
import java.net.URL;
import java.util.Properties;
-import jalview.bin.Console;
-
public class LaunchUtils
{
-
// setting these is LaunchUtils so don't need to import Platform
public final static boolean isMac = System.getProperty("os.name")
.indexOf("Mac") > -1;
return null;
} catch (IOException e)
{
- jalview.bin.Console.errPrintln(e.getMessage());
+ ErrorLog.errPrintln(e.getMessage());
return null;
}
}
try
{
URL localFileURL = new URL(buildDetails);
- InputStream in = localFileURL.openStream();
+ InputStream in = HttpUtils.openStream(localFileURL);
Properties buildProperties = new Properties();
buildProperties.load(in);
in.close();
null);
if (JCV == null)
{
- Console.errPrintln(
- "Could not obtain JAVA_COMPILE_VERSION for comparison");
+ ErrorLog.errPrintln("Could not obtain JAVA_COMPILE_VERSION for comparison");
return -2;
}
JAVA_COMPILE_VERSION = Integer.parseInt(JCV);
} catch (MalformedURLException e)
{
- jalview.bin.Console.errPrintln("Could not find " + buildDetails);
+ ErrorLog.errPrintln("Could not find " + buildDetails);
return -3;
} catch (IOException e)
{
- jalview.bin.Console.errPrintln("Could not load " + buildDetails);
+ ErrorLog.errPrintln("Could not load " + buildDetails);
return -4;
} catch (NumberFormatException e)
{
- jalview.bin.Console
- .errPrintln("Could not parse JAVA_COMPILE_VERSION");
+ ErrorLog.errPrintln("Could not parse JAVA_COMPILE_VERSION");
return -5;
}
String JV = System.getProperty("java.version");
if (JV == null)
{
- Console.errPrintln("Could not obtain java.version for comparison");
+ ErrorLog.errPrintln("Could not obtain java.version for comparison");
return -2;
}
if (JV.startsWith("1."))
: Integer.parseInt(JV.substring(0, JV.indexOf(".")));
} catch (NumberFormatException e)
{
- jalview.bin.Console.errPrintln("Could not parse java.version");
+ ErrorLog.errPrintln("Could not parse java.version");
return -3;
}
return JAVA_VERSION;
if (java_compile_version <= 0 || java_version <= 0)
{
- Console.errPrintln("Could not make Java version check");
+ ErrorLog.errPrintln("Could not make Java version check");
return true;
}
// Warn if these java.version and JAVA_COMPILE_VERSION conditions exist
jv.clear();
if (DEBUG)
{
- jalview.bin.Console.errPrintln("Array from '" + delimiter
+ ErrorLog.errPrintln("Array from '" + delimiter
+ "' separated List:\n" + v.length);
for (int i = 0; i < v.length; i++)
{
- jalview.bin.Console.errPrintln("item " + i + " '" + v[i] + "'");
+ ErrorLog.errPrintln("item " + i + " '" + v[i] + "'");
}
}
return v;
}
if (DEBUG)
{
- jalview.bin.Console.errPrintln(
+ ErrorLog.errPrintln(
"Empty Array from '" + delimiter + "' separated List");
}
return null;
{
System.err
.println("Returning '" + separator + "' separated List:\n");
- jalview.bin.Console.errPrintln(v);
+ ErrorLog.errPrintln(v.toString());
}
return v.toString();
}
if (DEBUG)
{
- jalview.bin.Console.errPrintln(
+ ErrorLog.errPrintln(
"Returning empty '" + separator + "' separated List\n");
}
return "" + separator;
--- /dev/null
+package jalview.util;
+
+import jalview.bin.Cache;
+
+public class UserAgent
+{
+
+ public static String getUserAgent(String className)
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append("Jalview");
+ sb.append('/');
+ sb.append(Cache.getDefault("VERSION", "Unknown"));
+ sb.append(" (");
+ sb.append(System.getProperty("os.name"));
+ sb.append("; ");
+ sb.append(System.getProperty("os.arch"));
+ sb.append(' ');
+ sb.append(System.getProperty("os.name"));
+ sb.append(' ');
+ sb.append(System.getProperty("os.version"));
+ sb.append("; ");
+ sb.append("java/");
+ sb.append(System.getProperty("java.version"));
+ sb.append("; ");
+ sb.append("jalview/");
+ sb.append(ChannelProperties.getProperty("channel"));
+ if (className != null)
+ {
+ sb.append("; ");
+ sb.append(className);
+ }
+ String installation = Cache.applicationProperties
+ .getProperty("INSTALLATION");
+ if (installation != null)
+ {
+ sb.append("; ");
+ sb.append(installation);
+ }
+ sb.append(')');
+ sb.append(" help@jalview.org");
+ return sb.toString();
+ }
+
+ public static String getUserAgent()
+ {
+ return getUserAgent(null);
+ }
+
+}
*/
package jalview.ws.dbsources;
+import java.io.InputStream;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Locale;
+import java.util.Vector;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import com.stevesoft.pat.Regex;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
+import jalview.util.HttpUtils;
import jalview.util.StringUtils;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
-import jalview.xml.binding.embl.ROOT;
import jalview.xml.binding.uniprot.DbReferenceType;
import jalview.xml.binding.uniprot.Entry;
import jalview.xml.binding.uniprot.FeatureType;
import jalview.xml.binding.uniprot.PositionType;
import jalview.xml.binding.uniprot.PropertyType;
-import java.io.InputStream;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.stream.FactoryConfigurationError;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
-import com.stevesoft.pat.Regex;
-
/**
* This class queries the Uniprot database for sequence data, unmarshals the
* returned XML, and converts it to Jalview Sequence records (including attached
// String downloadstring = getDomain() + queries + ".json";
URL url = new URL(downloadstring);
- URLConnection urlconn = url.openConnection();
+ URLConnection urlconn = HttpUtils.openConnection(url);
InputStream istr = urlconn.getInputStream();
List<Entry> entries = getUniprotEntries(istr);
if (entries != null)
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
+import jalview.util.HttpUtils;
import jalview.util.StringUtils;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
import jalview.xml.binding.uniprot.DbReferenceType;
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
- String downloadstring = getDomain() + "/uniprotkb/" + queries + ".xml";
+ String downloadstring = getDomain() + "/uniprotkb/" + queries
+ + ".xml";
URL url = new URL(downloadstring);
- HttpURLConnection urlconn = (HttpURLConnection) url.openConnection();
+ HttpURLConnection urlconn = HttpUtils.openConnection(url);
// anything other than 200 means we don't have data
// TODO: JAL-3882 reuse the EnsemblRestClient's fair
// use/backoff logic to retry when the server tells us to go away
*/
package jalview.ws.ebi;
-import java.util.Locale;
-
-import jalview.datamodel.DBRefSource;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
+import java.util.Locale;
import java.util.StringTokenizer;
+import jalview.datamodel.DBRefSource;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
/**
* DOCUMENT ME!
*
try
{
URL rcall = new URL(url);
- HttpURLConnection conn = (HttpURLConnection) rcall.openConnection();
+ HttpURLConnection conn = HttpUtils.openConnection(rcall);
int responseCode = conn.getResponseCode();
if (responseCode == 200)
{
*/
package jalview.ws.jws1;
-import jalview.datamodel.AlignmentI;
-import jalview.io.FileFormat;
-import jalview.io.FileParse;
-import jalview.io.FormatAdapter;
-import jalview.io.InputStreamParser;
-import jalview.util.MessageManager;
-
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.net.URLEncoder;
import java.util.Iterator;
+import jalview.datamodel.AlignmentI;
+import jalview.io.FileFormat;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.InputStreamParser;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
+
public class Annotate3D
{
// protected BufferedReader in;
"http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
+ content);
BufferedReader is = new BufferedReader(
- new InputStreamReader(url.openStream()));
+ new InputStreamReader(HttpUtils.openStream(url)));
String str4;
while ((str4 = is.readLine()) != null)
{
*/
package jalview.ws.jws2;
-import jalview.bin.Console;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
-
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import compbio.data.msa.JABAService;
import compbio.ws.client.Jws2Client;
import compbio.ws.client.Services;
+import jalview.bin.Console;
+import jalview.util.HttpUtils;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
/**
* @author JimP
try
{
URL url = new URL(server);
- url.openStream().close();
+ HttpUtils.openStream(url).close();
result = true;
} catch (MalformedURLException e)
{
*/
package jalview.ws.sifts;
-import java.util.Locale;
-
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import jalview.util.Format;
+import jalview.util.HttpUtils;
import jalview.util.Platform;
import jalview.xml.binding.sifts.Entry;
import jalview.xml.binding.sifts.Entry.Entity;
// siftsFileFTPURL);
// long now = System.currentTimeMillis();
URL url = new URL(siftsFileFTPURL);
- URLConnection conn = url.openConnection();
+ URLConnection conn = HttpUtils.openConnection(url);
InputStream inputStream = conn.getInputStream();
FileOutputStream outputStream = new FileOutputStream(downloadTo);
byte[] buffer = new byte[BUFFER_SIZE];
package jalview.ws.utils;
-import jalview.util.Platform;
-
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
+import jalview.util.HttpUtils;
+import jalview.util.Platform;
+
public class UrlDownloadClient
{
/**
temp = Files.createTempFile(".jalview_", ".tmp");
URL url = new URL(urlstring);
- rbc = Channels.newChannel(url.openStream());
+ rbc = Channels.newChannel(HttpUtils.openStream(url));
fos = new FileOutputStream(temp.toString());
fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
import java.awt.Dimension;
import java.awt.Font;
import java.awt.FontMetrics;
+import java.awt.event.MouseEvent;
import java.lang.reflect.InvocationTargetException;
import javax.swing.SwingUtilities;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import jalview.util.Platform;
import jalview.viewmodel.ViewportRanges;
public class AlignmentPanelTest
@Test(groups = { "Functional", "Not-bamboo" })
public void testGetVisibleWidth()
{
+ double scaling = jalview.gui.JvSwingUtilsTest.getScaling(af.alignPanel);
/*
* width for onscreen rendering is IDPanel width
*/
int w = af.alignPanel.getVisibleIdWidth(true);
assertEquals(w, af.alignPanel.getIdPanel().getWidth());
- assertEquals(w, 115);
+
+ // different scaling (1.0, 2.0) gives different results
+ int expectedWidth = scaling == 1.0 ? 112 : Platform.isMac() ? 115 : 107;
+ assertEquals(w, expectedWidth);
/*
* width for offscreen rendering is the same
* preference for auto id width overrides fixed width
*/
Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
- assertEquals(115, af.alignPanel.getVisibleIdWidth(false));
+ w = af.alignPanel.getVisibleIdWidth(false);
+ // allow some leeway for different OS renderings
+ assertTrue(w > 105 && w < 120);
+ // different scaling (1.0, 2.0) gives different results
+ assertEquals(w, expectedWidth);
}
@Test(groups = { "Functional", "Not-bamboo" })
public void testresetIdWidth()
{
+ double scaling = jalview.gui.JvSwingUtilsTest.getScaling(af.alignPanel);
/*
* width for onscreen rendering is IDPanel width
*/
int w = af.alignPanel.getVisibleIdWidth(true);
- assertEquals(w, af.alignPanel.getIdPanel().getWidth());
- assertEquals(w, 115);
+ int actual = af.alignPanel.getIdPanel().getWidth();
+ assertEquals(w, actual);
+ // allow some leeway for different OS renderings
+ assertTrue(w > 105 && w < 120);
+ // different scaling (1.0, 2.0) gives different results
+ int expectedWidth = scaling == 1.0 ? 112 : Platform.isMac() ? 115 : 107;
+ assertEquals(w, expectedWidth);
// manually adjust
af.viewport.setIdWidth(200);
+ // fake mouse drag sets manuallyAdjusted to true (0,0 not moving mouse)
+ MouseEvent drag = new MouseEvent(af.alignPanel,
+ MouseEvent.MOUSE_DRAGGED, System.currentTimeMillis(), 0, 0, 0,
+ MouseEvent.BUTTON1, false);
+ af.alignPanel.idwidthAdjuster.mouseDragged(drag);
+ af.alignPanel.paintComponent(af.alignPanel.getGraphics());
w = af.alignPanel.calculateIdWidth().width;
assertTrue(
af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
- assertEquals(w, af.alignPanel.getIdPanel().getWidth());
+ actual = af.alignPanel.getIdPanel().getWidth();
+ assertEquals(w, actual);
af.viewport.setIdWidth(-1);
+ af.alignPanel.calculateIdWidth();
af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(false);
w = af.alignPanel.calculateIdWidth().width;
+ af.alignPanel.paintComponent(af.alignPanel.getGraphics());
- assertEquals(w, af.alignPanel.getIdPanel().getWidth());
+ actual = af.alignPanel.getIdPanel().getWidth();
+ assertEquals(w, actual);
- assertNotEquals(w, 115);
+ // setting a negative IdWidth and then running calculateIdWidth resets width
+ // to optimal id width
+ // allow some leeway for different OS renderings
+ assertTrue(w > 105 && w < 120);
+ // different scaling (1.0, 2.0) gives different results
+ assertEquals(w, expectedWidth);
}
@Test(groups = "Functional")
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.structure.StructureImportSettings.TFType;
+import jalview.util.Platform;
public class AnnotationLabelsTest2
{
+ private static double scaling;
+
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
*/
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Jalview.main(new String[] { "--nonews", "--nosplash", });
+
+ scaling = JvSwingUtilsTest.getScaling(Desktop.instance);
}
@AfterMethod(alwaysRun = true)
{
AlignFrame af = new FileLoader()
.LoadFileWaitTillLoaded(alignmentFilename, DataSourceType.FILE);
+
try
{
Thread.sleep(200); // to allow alignment annotations to open
idWidth = av.getIdWidth();
assertTrue(idWidth > idWidth1min,
"idWidth (" + idWidth + ") is not greater than " + idWidth1min);
- assertTrue(idWidth < idWidth1max,
- "idWidth (" + idWidth + ") is not narrower than" + idWidth1max);
+ assertTrue(idWidth < idWidth1max, "idWidth (" + idWidth
+ + ") is not narrower than " + idWidth1max);
// set wrap
if (wrap)
// idWidth = ap.getIdPanel().getWidth();
idWidth = av.getIdWidth();
- assertTrue(idWidth > idWidth2min,
+ assertTrue(idWidth >= idWidth2min,
"idWidth (" + idWidth + ") is not greater than " + idWidth2min);
- assertTrue(idWidth < idWidth2max,
- "idWidth (" + idWidth + ") is not narrower than" + idWidth2max);
+ assertTrue(idWidth <= idWidth2max, "idWidth (" + idWidth
+ + ") is not narrower than " + idWidth2max);
}
@Test(
AlignViewport av = af.getCurrentView();
int idWidth = 0;
-
idWidth = av.getIdWidth();
assertTrue(idWidth > idWidth1min,
"idWidth (" + idWidth + ") is not greater than " + idWidth1min);
int idWidth2min,
int idWidth2max,
*/
+ int idWidth2min = scaling == 1.0 ? 114 : 108;
+ int idWidth2max = scaling == 1.0 ? 117 : 114; // was 130
+ if (Platform.isMac())
+ {
+ idWidth2max = 122;
+ }
+
return new Object[][] {
//
/*
100,
"./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb",
"./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json",
- true, TFType.PLDDT, null, 115, 130 },
+ true, TFType.PLDDT, null, idWidth2min, idWidth2max },
{ "./test/files/annotation_label_width/sample.a2m", true, 50, 70,
100,
"./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb",
"./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json",
- true, TFType.PLDDT, null, 115, 130 },
+ true, TFType.PLDDT, null, idWidth2min, idWidth2max },
/*
*/
};
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import java.awt.Component;
+import java.awt.Graphics2D;
+import java.awt.geom.AffineTransform;
+
import javax.swing.JScrollBar;
import org.testng.annotations.BeforeClass;
JvSwingUtils.wrapTooltip(true, tip));
assertEquals(expected, JvSwingUtils.wrapTooltip(false, tip));
}
+
+ public static double getScaling(Component c)
+ {
+ Graphics2D g = (Graphics2D) c.getGraphics();
+ if (g == null)
+ {
+ return 0.0;
+ }
+ AffineTransform t = g.getTransform();
+ double scaling = t.getScaleX(); // Assuming square pixels :P
+ return scaling;
+ }
+
}
*/
package jalview.gui;
-import java.awt.Font;
-import java.awt.FontMetrics;
-
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
+import java.awt.Font;
+import java.awt.FontMetrics;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.io.DataSourceType;
-import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-
import junit.extensions.PA;
public class SeqCanvasTest
av.setScaleRightWrapped(true);
FontMetrics fm = testee.getFontMetrics(av.getFont());
int labelWidth = fm.stringWidth("000") + charWidth;
- assertEquals(labelWidth, 39); // 3 x 9 + charWidth
+ // some leeway for different OS rendering of text
+ assertTrue(labelWidth >= 36 && labelWidth <= 39);
/*
* width 400 pixels leaves (400 - 2*labelWidth) for residue columns
av.setScaleLeftWrapped(false);
wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
canvasHeight);
- assertEquals(wrappedWidth, 23);
+ // some leeway for different OS rendering of text
+ assertTrue(wrappedWidth >= 22 && wrappedWidth <= 23);
+ int difference = wrappedWidth - 23;
/*
* add 10 pixels to width to fit in another whole residue column
canvasWidth += 1;
wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
canvasHeight);
- assertEquals(wrappedWidth, 24);
+ assertEquals(wrappedWidth, 24 + difference);
/*
* turn off East scale to gain 39 more pixels (3 columns remainder 3)
av.setScaleRightWrapped(false);
wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
canvasHeight);
- assertEquals(wrappedWidth, 27);
+ assertEquals(wrappedWidth, 27 + difference);
/*
* add 9 pixels to width to gain a residue column
canvasWidth += 1;
wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
canvasHeight);
- assertEquals(wrappedWidth, 28); // 9px is enough
+ assertEquals(wrappedWidth, 28 + difference); // 9px is enough
/*
* now West but not East scale - lose 39 pixels or 4 columns
canvasWidth += 1;
wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
canvasHeight);
- assertEquals(wrappedWidth, 25); // 3px is enough
+ assertEquals(wrappedWidth, 25 + difference); // 3px is enough
/*
* turn off scales left and right, make width exactly 157 columns
av.setScaleRightWrapped(true);
FontMetrics fm = testee.getFontMetrics(av.getFont());
int labelWidth = fm.stringWidth("000") + charWidth;
- assertEquals(labelWidth, 39); // 3 x 9 + charWidth
+ // some leeway for different OS rendering of text
+ assertTrue(labelWidth >= 36 && labelWidth <= 39);
int annotationHeight = testee.getAnnotationHeight();
/*
assertEquals(charHeight, 17);
assertEquals(charWidth, 12);
+ double scaling = JvSwingUtilsTest.getScaling(alignFrame.alignPanel);
+
FontMetrics fm = testee.getFontMetrics(av.getFont());
int labelWidth = fm.stringWidth("00000") + charWidth;
- assertEquals(labelWidth, 57); // 5 x 9 + charWidth
+ // some leeway for different OS rendering of text
+ assertTrue(labelWidth >= 52 && labelWidth <= 57);
assertEquals(testee.seqCanvas.getLabelWidthWest(), labelWidth);
int x = 0;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import java.io.FileNotFoundException;
+
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
@Test(groups = { "Functional" }, dataProvider = "identifyFiles")
public void testIdentify(String data, FileFormatI expectedFileType)
- throws FileFormatException
+ throws FileFormatException, FileNotFoundException
{
DataSourceType protocol = DataSourceType.FILE;
IdentifyFile ider = new IdentifyFile();
* @throws FileFormatException
*/
@Test(groups = "Functional")
- public void testIdentify_featureFile() throws FileFormatException
+ public void testIdentify_featureFile()
+ throws FileFormatException, FileNotFoundException
{
IdentifyFile ider = new IdentifyFile();
// non-numeric start column:
assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t.\tss"));
}
+
+ @Test(groups = "Network", dataProvider = "urlTargetsAndExceptions")
+ public void testExceptions(String url,
+ Class<? extends Exception> expectedExceptionClass,
+ FileFormatI expectedFormat)
+ {
+ Class<? extends Exception> actualExceptionClass = null;
+ FileFormatI actualFormat = null;
+ try
+ {
+ actualFormat = new IdentifyFile().identify(url, DataSourceType.URL);
+ } catch (FileFormatException | FileNotFoundException e)
+ {
+ Assert.assertNull(expectedFormat,
+ "Exception occurred when expecting an identifiable format.");
+ Assert.assertNotNull(expectedExceptionClass,
+ "An unexpected exception occurred: '" + e.getMessage() + "'");
+ Assert.assertEquals(e.getClass(), expectedExceptionClass,
+ "Got the wrong kind of exception.");
+ actualExceptionClass = e.getClass();
+ }
+
+ if (expectedExceptionClass != null)
+ {
+ Assert.assertEquals(actualExceptionClass, expectedExceptionClass,
+ "Expected an exception but got the wrong one.");
+ }
+
+ }
+
+ @DataProvider(name = "urlTargetsAndExceptions")
+ public Object[][] urlTargetsAndExceptions()
+ {
+ /*
+ String targetUrl,
+ String finalUrl,
+ String foundInFirstLine,
+ */
+ return new Object[][] {
+ //
+ /*
+ { "http://jalview.org/examples/uniref50.fa", null,
+ FileFormat.Fasta },
+ { "https://www.jalview.org/examples/NOFILE.fa",
+ FileNotFoundException.class, null },
+ { "https://NOSERVER.jalview.org/", FileNotFoundException.class,
+ null },
+ */
+ { "https://www.jalview.org/schools/Jalview_Schools_Workbook_200.jpg",
+ FileFormatException.class, null },
+ /*
+ */
+ //
+ };
+ }
+
}
import java.awt.Rectangle;
import java.io.File;
import java.io.IOException;
-import java.math.BigInteger;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
import jalview.schemes.TCoffeeColourScheme;
import jalview.structure.StructureImportSettings;
import jalview.util.MapList;
-import jalview.util.Platform;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
boolean diffseqcols = false, diffgseqcols = false;
SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
- for (int p = 0, pSize = af.getViewport().getAlignment()
- .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0,
+ pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+ && (!diffseqcols || !diffgseqcols); p++)
{
if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
.findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
assertTrue(__rcs.isSeqAssociated(),
"Group Annotation colourscheme wasn't sequence associated");
- for (int p = 0, pSize = af.getViewport().getAlignment()
- .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0,
+ pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+ && (!diffseqcols || !diffgseqcols); p++)
{
if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
assertEquals(ov1.getCanvas().getResidueColour(), Color.white);
assertEquals(ov1.getCanvas().getHiddenColour(), Color.yellow);
assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original");
- assertEquals(ov1.getFrameBounds(), new Rectangle(20, 30, 200, 400));
+
+ double scaling = jalview.gui.JvSwingUtilsTest.getScaling(ov1);
+ // int width = scaling == 1.0 ? 225 : 200;
+ // int width = scaling == 1.0 ? 225 : 200;
+ Rectangle ov1Rectangle = ov1.getFrameBounds();
+ assertEquals(ov1Rectangle,
+ new Rectangle(20, 30, ov1Rectangle.width, 400));
+ int width = ov1Rectangle.width;
+ assertTrue(width >= 200 && width <= 225,
+ "Rectangle width was not in the range expected (200<=width<=225; width="
+ + width + ")");
assertTrue(ov1.isShowHiddenRegions());
}
assertNotNull(af, "Didn't read in the example file correctly.");
// FIXME JAL-4281 test made platform dependent to pass, but probably
// shouldn't be platform dependent
- assertEquals(af.alignPanel.getAlignViewport().getIdWidth(),
- Platform.isAMacAndNotJS() ? 144 : 138,
- "Legacy project import should have fixed ID width");
+ int idWidth = af.alignPanel.getAlignViewport().getIdWidth();
+ double scaling = jalview.gui.JvSwingUtilsTest.getScaling(af.alignPanel);
+ // int expectedWidth = Platform.isMac() ? 144 : Platform.isLinux() ? scaling
+ // == 1.0 ? 131 : 128 : 138;
+ int minExpectedWidth = 128;
+ int maxExpectedWidth = 144;
+ assertTrue(minExpectedWidth <= idWidth && maxExpectedWidth >= idWidth,
+ "Legacy project import should have fixed ID width. Not within the expected range ("
+ + minExpectedWidth + "-" + maxExpectedWidth + ")");
assertTrue(
af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
};
}
+ @Test(
+ groups = "Functional",
+ dataProvider = "stringFilenamesBaseAndExtensionsData")
+ public void stringGetBaseAndExtensionTest(String filename,
+ String extension, String base)
+ {
+ String thisBase = FileUtils.getBase(filename);
+ Assert.assertEquals(thisBase, base,
+ "base part of path and filename not as expected");
+ String thisExtension = FileUtils.getExtension(filename);
+ Assert.assertEquals(thisExtension, extension,
+ "extension part of filename not as expected");
+ }
+
+ @DataProvider(name = "stringFilenamesBaseAndExtensionsData")
+ public Object[][] stringFilenamesBaseAndExtensionsData()
+ {
+ return new Object[][] {
+ /*
+ * String full URL or path
+ * String base the above but without the extension if there is one
+ * String extension the filename extension if there is one
+ */
+ /*
+ */
+ { "/examples/uniref50.fa", "fa", "/examples/uniref50." },
+ { "/examples/uniref50", null, "/examples/uniref50" },
+ { "/examples/.uniref50", null, "/examples/.uniref50" },
+ { "/exampl.es/uniref50", null, "/exampl.es/uniref50" },
+ { "/examples/uniref50.", "", "/examples/uniref50." },
+ { "examples/uniref50.fa", "fa", "examples/uniref50." },
+ { "examples/uniref50", null, "examples/uniref50" },
+ { "examples/.uniref50", null, "examples/.uniref50" },
+ { "exampl.es/uniref50", null, "exampl.es/uniref50" },
+ { "examples/uniref50.", "", "examples/uniref50." },
+ { "https://www.jalview.org:443/examples/uniref50.fa", "fa",
+ "https://www.jalview.org:443/examples/uniref50." },
+ { "https://www.jalview.org:443/examples/uniref50", null,
+ "https://www.jalview.org:443/examples/uniref50" },
+ { "https://www.jalview.org:443/examples/.uniref50", null,
+ "https://www.jalview.org:443/examples/.uniref50" },
+ { "https://www.jalview.org:443/exampl.es/uniref50", null,
+ "https://www.jalview.org:443/exampl.es/uniref50" },
+ { "https://www.jalview.org:443/examples/uniref50.", "",
+ "https://www.jalview.org:443/examples/uniref50." },
+ /*
+ */
+ //
+ };
+ }
}
--- /dev/null
+package jalview.util;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.Locale;
+
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+public class HttpUtilsTest
+{
+ @Test(groups = { "Network" }, dataProvider = "urlTargetsAndDestinations")
+ public void testFollowConnection(String targetUrl, String finalUrl,
+ String notUsed0, String notUsed1) throws IOException
+ {
+ URL tUrl = new URL(targetUrl);
+ URL fUrl = new URL(finalUrl);
+ HttpURLConnection conn1 = HttpUtils
+ .followConnection((HttpURLConnection) tUrl.openConnection());
+ URL url1 = conn1.getURL();
+ Assert.assertEquals(url1, fUrl, "Final URL is not the same.");
+ }
+
+ @Test(groups = { "Network" }, dataProvider = "urlTargetsAndDestinations")
+ public void testOpenConnection(String targetUrl, String finalUrl,
+ String notUsed0, String notUsed1) throws IOException
+ {
+ URL tUrl = new URL(targetUrl);
+ URL fUrl = new URL(finalUrl);
+ HttpURLConnection conn1 = HttpUtils.openConnection(tUrl);
+ URL url1 = conn1.getURL();
+ Assert.assertEquals(url1, fUrl, "Final URL is not the same.");
+ }
+
+ @Test(groups = { "Network" }, dataProvider = "urlTargetsAndDestinations")
+ public void testOpenStream(String targetUrl, String finalUrl,
+ String inFirstLine, String inDocument) throws IOException
+ {
+ URL tUrl = new URL(targetUrl);
+ URL fUrl = new URL(finalUrl);
+ InputStream is1 = HttpUtils.openStream(tUrl);
+ BufferedReader br1 = new BufferedReader(new InputStreamReader(is1));
+ String firstLine = br1.readLine().toLowerCase(Locale.ROOT);
+ Assert.assertTrue(
+ firstLine.contains(inFirstLine.toLowerCase(Locale.ROOT)),
+ "First line of text '" + firstLine + "' does not contain '"
+ + inFirstLine + "'");
+ String inDocumentLC = inDocument.toLowerCase(Locale.ROOT);
+ boolean found = false;
+ String line = null;
+ while ((line = br1.readLine()) != null)
+ {
+ if (line.toLowerCase(Locale.ROOT).contains(inDocumentLC))
+ {
+ found = true;
+ break;
+ }
+ }
+ Assert.assertTrue(found,
+ "Text '" + inDocument + "' not found in '" + finalUrl + "'");
+ }
+
+ @DataProvider(name = "urlTargetsAndDestinations")
+ public Object[][] urlTargetsAndDestinations()
+ {
+ /*
+ String targetUrl, // the URL you ask for
+ String finalUrl, // the URL you end up at
+ String foundInFirstLine, // some text found in the first line
+ String foundInDocument, // some text found in the document (and won't be in an error page)
+ */
+ return new Object[][] {
+ //
+ /*
+ */
+ { "http://jalview.org/", "https://www.jalview.org/", "<!doctype",
+ "Jalview is a" },
+ { "http://www.jalview.org/", "https://www.jalview.org/",
+ "<!doctype", "Jalview is a" },
+ { "https://jalview.org", "https://www.jalview.org/", "<!doctype",
+ "Jalview is a" },
+ /*
+ */
+ //
+ };
+ }
+
+}
#!/usr/bin/env bash
# perform a dev build and install on local macOS machine
-INSTALLERVOL="Jalview Non-Release Installer"
-APP="Jalview Local.app"
-
+APP=""
+INSTALLERVOL=""
APPLICATIONS=/Applications
-CHANNEL=NOCHANNEL
+CHANNEL="LOCAL"
DMG=build/install4j/11/Jalview_Local-TEST-macos-java_11.dmg
+GRADLE=""
+APPBASEOVERRIDEARG=""
+MEDIA=macosArchive
+CLEAN="clean"
+JAVA=11
+x=$(grep jalview.version= RELEASE)
+VERSION=${x#*=}
+
+while getopts ":i:n:a:c:d:go:m:j:l" opt; do
+ case ${opt} in
+ i)
+ INSTALLERVOL="${OPTARG}"
+ ;;
+ n)
+ APP="${OPTARG}"
+ ;;
+ a)
+ APPLICATIONS="${OPTARG}"
+ ;;
+ c)
+ CHANNEL="${OPTARG}"
+ ;;
+ d)
+ DMG="${OPTARG}"
+ ;;
+ g)
+ GRADLE=1
+ ;;
+ o)
+ APPBASEOVERRIDEARG="-Pgetdown_appbase_override=${OPTARG}"
+ ;;
+ m)
+ MEDIA="${OPTARG}"
+ ;;
+ j)
+ JAVA="${OPTARG}"
+ ;;
+ l)
+ CLEAN=""
+ ;;
+ ?)
+ echo "Invalid option -${OPTARG}"
+ exit 1;
+ ;;
+ esac
+done
+if [ -z $APP ]; then
+ ARCH=x64
+ if [ $(uname -m) = "arm64" ]; then
+ ARCH=aarch64
+ fi
+ OS=macos
+ case $(uname -o) in
+ Darwin)
+ OS=macos
+ ;;
+ Windows)
+ OS=windows
+ ;;
+ Linux)
+ OS=linux
+ ;;
+ *)
+ OS=unix
+ ;;
+ esac
+ case ${CHANNEL} in
+ DEVELOP)
+ APP="Jalview Develop"
+ DMG="build/install4j/11/${APP// /_}-${VERSION//\./_}-d$(date +%Y%m%d)-${OS}-${ARCH}-java_${JAVA}.dmg"
+ ;;
+ TEST-RELEASE)
+ APP="Jalview Test"
+ DMG="build/install4j/11/${APP// /_}-${VERSION//\./_}-test-${OS}-${ARCH}-java_${JAVA}.dmg"
+ ;;
+ RELEASE)
+ APP="Jalview"
+ DMG="build/install4j/11/${APP// /_}-${VERSION//\./_}-${OS}-${ARCH}-java_${JAVA}.dmg"
+ ;;
+ *)
+ APP="Jalview Local"
+ DMG=build/install4j/11/${APP// /_}-TEST-macos-java_11.dmg
+ ;;
+ esac
+fi
+if [ -z $INSTALLERVOL ]; then
+ INSTALLERVOL="${APP} Installer"
+fi
-if [ x$1 != "xnogradle" ]; then
- gradle installers -PCHANNEL=LOCAL -Pinstall4j_media_types=macosArchive
+if [ "${GRADLE}" = 1 ]; then
+ echo "Running: gradle ${CLEAN} installers -PCHANNEL="${CHANNEL}" -Pinstall4j_media_types="${MEDIA}" ${APPBASEOVERRIDEARG} -PJAVA_VERSION=${JAVA}"
+ gradle ${CLEAN} installers -PCHANNEL="${CHANNEL}" -Pinstall4j_media_types="${MEDIA}" ${APPBASEOVERRIDEARG} -PJAVA_VERSION=${JAVA}
else
echo "Not running gradle installers"
fi
if [ $? = 0 ]; then
- umount "/Volumes/$INSTALLERVOL"
+ if [ -e "/Volumes/$INSTALLERVOL" ]; then
+ hdiutil detach "/Volumes/$INSTALLERVOL"
+ fi
if [ -e "$DMG" ]; then
open $DMG
else
echo "No DMG file '$DMG'" 1>&2
- exit 1
+ exit 2
fi
echo "Mounting '$DMG' at /Volumes"
N=0
- while [ \! -e "/Volumes/$INSTALLERVOL/$APP" ]; do
- if [ $(( N%1000 )) = 0 ]; then
- echo -n "."
- fi
+ MOUNTEDAPP="/Volumes/$INSTALLERVOL/$APP.app"
+ echo "Waiting for '$MOUNTEDAPP' to appear"
+ while [ \! -e "$MOUNTEDAPP" ]; do
+ echo -n "."
N=$(( N+1 ))
+ if [ $N = 40 ]; then
+ echo ""
+ echo "Looks like something wrong with the DMG '$DMG'"
+ exit 4
+ fi
+ sleep 0.1
done
echo ""
+else
+ echo "Problem with gradle build: exit code $?"
+ exit 3
fi
-if [ -e "/Volumes/$INSTALLERVOL/$APP" ]; then
- echo "Removing '$APPLICATIONS/$APP'"
- /bin/rm -r "$APPLICATIONS/$APP"
- echo "Syncing '/Volumes/$INSTALLERVOL/$APP' to '$APPLICATIONS/'"
- rsync -avh "/Volumes/$INSTALLERVOL/$APP" "$APPLICATIONS/"
+
+if [ -e "$MOUNTEDAPP" ]; then
+ echo "Removing '$APPLICATIONS/$APP.app'"
+ /bin/rm -r "$APPLICATIONS/$APP.app"
+ echo "Syncing '$MOUNTEDAPP' to '$APPLICATIONS/'"
+ rsync -avh "$MOUNTEDAPP" "$APPLICATIONS/"
echo "Unmounting '/Volumes/$INSTALLERVOL'"
- umount "/Volumes/$INSTALLERVOL"
+ hdiutil detach "/Volumes/$INSTALLERVOL"
fi
};
my @dontaddshortname = qw(features json);
-my @dontaddextension = qw(html xml json jar mfa fastq);
+# mfa and fastq not properly supported in Jalview (but enough to be in the application extensions)
+# ENA flatfile extension txt is too generic, as well as html xml json jar
+my @dontaddextension = qw(txt html xml json jar mfa fastq);
my $add_associations = {
biojson => {shortname=>"biojson",name=>"BioJSON",extensions=>["biojson"]},
gff2 => {shortname=>"gff2",name=>"Generic Features Format v2",extensions=>["gff2"]},
my @put_first = qw(jalview jvl);
my @owner = @put_first;
-my @non_primary = qw(mmcif mmcif2 pdb);
+my @non_primary = qw(mmcif mmcif2 pdb txt);
my $v = ($i4jversion >= 8)?$i4jversion:"";
my $i4jtemplatefile = "file_associations_template-install4j${v}.xml";
+++ /dev/null
-#!/usr/bin/env perl
-
-use strict;
-
-my $i4jversion = 8;
-if ($ARGV[0] eq "-v") {
- shift @ARGV;
- $i4jversion = shift @ARGV;
- die("-v i4jversion must be an integer [probably 7 or 8]") unless $i4jversion =~ m/^\d+$/;
-}
-
-my $fileformats = $ARGV[0];
-$fileformats = "../../src/jalview/io/FileFormat.java" unless $fileformats;
-
-# default mimetype will be text/x-$shortname
-# TODO: find an actual extension for mat, see JAL-Xxxxx for outstanding issues too
-# TODO: look up standard mime type used for BLASTfmt matrices, etc
-my $mimetypes = {
- rnaml => "application/rnaml+xml",
- biojson => "application/x-jalview-biojson+json",
- jnet => "application/x-jalview-jnet+text",
- features => "application/x-jalview-features+text",
- scorematrix => "application/x-jalview-scorematrix+text",
- pdb => "chemical/x-pdb",
- mmcif => "chemical/x-cif",
- mmcif2 => "chemical/x-mmcif",
- jalview => "application/x-jalview+xml+zip",
- jvl => "application/x-jalview-jvl+text",
- annotations => "application/x-jalview-annotations+text",
-};
-
-my @dontaddshortname = qw(features json);
-my @dontaddextension = qw(html xml json jar mfa fastq);
-my $add_associations = {
- biojson => {shortname=>"biojson",name=>"BioJSON",extensions=>["biojson"]},
- gff2 => {shortname=>"gff2",name=>"Generic Features Format v2",extensions=>["gff2"]},
- gff3 => {shortname=>"gff3",name=>"Generic Features Format v3",extensions=>["gff3"]},
- features => {shortname=>"features",name=>"Jalview Features",extensions=>["features","jvfeatures"]},
- annotations => {shortname=>"annotations",name=>"Jalview Annotations",extensions=>["annotations","jvannotations"]},
- mmcif => {shortname=>"mmcif",name=>"CIF",extensions=>["cif"]},
- mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
- jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"jvl_file"},
- jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
- scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
-};
-my $add_extensions = {
- blc => ["blc"],
-};
-my @put_first = qw(jalview jvl);
-
-my @non_primary = qw(mmcif mmcif2 pdb);
-
-my $v = ($i4jversion >= 8)?$i4jversion:"";
-my $i4jtemplatefile = "file_associations_template-install4j${v}.xml";
-my $i4jtemplate;
-my $mactemplatefile = "file_associations_template-Info_plist.xml";
-my $mactemplate;
-
-open(MT,"<$mactemplatefile") or die("Could not open '$mactemplatefile' for reading");
-while(<MT>){
- $mactemplate .= $_;
-}
-close(MT);
-open(IT,"<$i4jtemplatefile") or die("Could not open '$i4jtemplatefile' for reading");
-while(<IT>){
- $i4jtemplate .= $_;
-}
-close(IT);
-my $macauto;
-my $i4jauto;
-
-my $macautofile = $mactemplatefile;
-$macautofile =~ s/template/auto$1/;
-
-my $i4jautofile = $i4jtemplatefile;
-$i4jautofile =~ s/template/auto$1/;
-
-for my $key (sort keys %$add_associations) {
- my $a = $add_associations->{$key};
- warn("Known file association for $a->{shortname} (".join(",",@{$a->{extensions}}).")\n");
-}
-
-open(MA,">$macautofile") or die ("Could not open '$macautofile' for writing");
-print MA "<key>CFBundleDocumentTypes</key>\n<array>\n\n";
-
-open(IA,">$i4jautofile") or die ("Could not open '$i4jautofile' for writing");
-
-open(IN, "<$fileformats") or die ("Could not open '$fileformats' for reading");
-my $id = 10000;
-my $file_associations = {};
-while(my $line = <IN>) {
- $line =~ s/\s+/ /g;
- $line =~ s/(^ | $)//g;
- if ($line =~ m/^(\w+) ?\( ?"([^"]*)" ?, ?"([^"]*)" ?, ?(true|false) ?, ?(true|false) ?\)$/i) {
- my $shortname = lc($1);
- next if (grep($_ eq $shortname, @dontaddshortname));
- my $name = $2;
- my $extensions = $3;
- $extensions =~ s/\s+//g;
- my @possextensions = map(lc($_),split(m/,/,$extensions));
- my @extensions;
- my $addext = $add_extensions->{$shortname};
- if (ref($addext) eq "ARRAY") {
- push(@possextensions, @$addext);
- }
- for my $possext (@possextensions) {
- next if grep($_ eq $possext, @extensions);
- next if grep($_ eq $possext, @dontaddextension);
- push(@extensions,$possext);
- }
- next unless scalar(@extensions);
- $file_associations->{$shortname} = {
- shortname => $shortname,
- name => $name,
- extensions => \@extensions
- };
- warn("Reading file association for $shortname (".join(",",@extensions).")\n");
- }
-}
-close(IN);
-
-my %all_associations = (%$file_associations, %$add_associations);
-
-my @ordered = (@put_first, @non_primary);
-for my $key (sort keys %all_associations) {
- next if grep($_ eq $key, @ordered);
- push(@ordered, $key);
-}
-my $num = $#ordered + 1;
-
-warn("--\n");
-
-my $i4jcount = 0;
-for my $shortname (@ordered) {
- my $a = $all_associations{$shortname};
- next if (ref($a) ne "HASH");
-
- my $name = $a->{name};
- my $extensions = $a->{extensions};
- my $mimetype = $mimetypes->{$shortname};
- $mimetype = "application/x-$shortname+txt" unless $mimetype;
-
- my $iconfile = $a->{iconfile};
- $iconfile = "Jalview-File" unless $iconfile;
-
- my $primary = (! grep($_ eq $shortname, @non_primary));
- my $primarystring = $primary?"true":"false";
- my $role = $primary?"Editor":"Viewer";
-
- my @extensions = @$extensions;
-
- my $xname = xml_escape($name);
- my $xmimetype = xml_escape($mimetype);
- my $xshortname = xml_escape($shortname);
- my $xiconfile = xml_escape($iconfile);
- my $xrole = xml_escape($role);
- my $xROLE = xml_escape(uc($role));
- my $xprimarystring = xml_escape($primarystring);
-
- my $macentry = $mactemplate;
- $macentry =~ s/\$\$NAME\$\$/$xname/g;
- $macentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
- $macentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
- $macentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
- $macentry =~ s/\$\$ROLE\$\$/$xrole/g;
- $macentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
- while ($macentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
- my $pre = $1;
- my $post = $2;
- my $macextensions;
- for my $ext (@extensions) {
- my $xext = xml_escape($ext);
- $macextensions .= $pre.$xext.$post;
- }
- $macentry =~ s/\$\$${pre}EXTENSIONS${post}\$\$/$macextensions/g;
- }
- print MA $macentry;
-
- my $i4jentry = $i4jtemplate;
- $i4jentry =~ s/\$\$NAME\$\$/$xname/g;
- $i4jentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
- $i4jentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
- $i4jentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
- $i4jentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
- $i4jentry =~ s/\$\$MACASSOCIATIONROLE\$\$/$xROLE/g;
-
- my $ext = join(",",sort(@extensions));
- my $xdisplayext = xml_escape(join(", ", map(".$_",sort(@extensions))));
- my $progresspercent = int(($i4jcount/$num)*100);
- $progresspercent = 100 if $progresspercent > 100;
- $i4jcount++;
- my $xext = xml_escape($ext);
- my $addunixextension = "true";
-
- $i4jentry =~ s/\$\$ADDUNIXEXTENSION\$\$/$addunixextension/g;
- $i4jentry =~ s/\$\$EXTENSION\$\$/$xext/g;
- $i4jentry =~ s/\$\$DISPLAYEXTENSION\$\$/$xdisplayext/g;
- $i4jentry =~ s/\$\$PROGRESSPERCENT\$\$/$progresspercent/g;
- $i4jentry =~ s/\$\$ID\$\$/$id/g;
- $id++;
- $i4jentry =~ s/\$\$ID1\$\$/$id/g;
- $id++;
- $i4jentry =~ s/\$\$ID2\$\$/$id/g;
- $id++;
-
- print IA $i4jentry;
-
- delete $all_associations{$shortname};
- warn("Writing entry for $name (".join(",",@$extensions).": $mimetype)\n");
-}
-
-close(IA);
-print MA "</array>\n";
-close(MA);
-
-sub xml_escape {
- my $x = shift;
- # stolen from Pod::Simple::XMLOutStream in base distro
- $x =~ s/([^-\n\t !\#\$\%\(\)\*\+,\.\~\/\:\;=\?\@\[\\\]\^_\`\{\|\}a-zA-Z0-9])/'&#'.(ord($1)).';'/eg;
- return $x;
-}
<dict>
<key>CFBundleTypeExtensions</key>
<array>
-<string>txt</string>
+<string>fa</string>
+<string>fasta</string>
</array>
<key>CFBundleTypeName</key>
-<string>ENA Flatfile File</string>
+<string>Fasta File</string>
<key>CFBundleTypeIconFile</key>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
-<string>application/x-embl+txt</string>
+<string>application/x-fasta+txt</string>
</array>
<key>LSIsAppleDefaultForType</key>
<true/>
<dict>
<key>CFBundleTypeExtensions</key>
<array>
-<string>fa</string>
-<string>fasta</string>
+<string>features</string>
+<string>jvfeatures</string>
</array>
<key>CFBundleTypeName</key>
-<string>Fasta File</string>
+<string>Jalview Features File</string>
<key>CFBundleTypeIconFile</key>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
-<string>application/x-fasta+txt</string>
+<string>application/x-jalview-features+text</string>
</array>
<key>LSIsAppleDefaultForType</key>
<true/>
<dict>
<key>CFBundleTypeExtensions</key>
<array>
-<string>features</string>
-<string>jvfeatures</string>
+<string>fc</string>
</array>
<key>CFBundleTypeName</key>
-<string>Jalview Features File</string>
+<string>Jalview Feature Settings File File</string>
<key>CFBundleTypeIconFile</key>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
-<string>application/x-jalview-features+text</string>
+<string>application/x-featuresettings+txt</string>
</array>
<key>LSIsAppleDefaultForType</key>
<true/>
</serializedBean>
</action>
- <action name="Jalview Launch (.jvl) progress bar 4" id="10004" customizedId="Jalview Launch-jvl-10004-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Launch (.jvl) progress bar 3" id="10004" customizedId="Jalview Launch-jvl-10004-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="4" />
+ <property name="percentValue" type="int" value="3" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="CIF (.cif) progress bar 8" id="10007" customizedId="CIF-cif-10007-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="CIF (.cif) progress bar 7" id="10007" customizedId="CIF-cif-10007-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="8" />
+ <property name="percentValue" type="int" value="7" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="mmCIF (.mcif, .mmcif) progress bar 12" id="10010" customizedId="mmCIF-mcif,mmcif-10010-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="mmCIF (.mcif, .mmcif) progress bar 11" id="10010" customizedId="mmCIF-mcif,mmcif-10010-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="12" />
+ <property name="percentValue" type="int" value="11" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="PDB (.ent, .pdb) progress bar 16" id="10013" customizedId="PDB-ent,pdb-10013-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PDB (.ent, .pdb) progress bar 15" id="10013" customizedId="PDB-ent,pdb-10013-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="16" />
+ <property name="percentValue" type="int" value="15" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="AMSA (.amsa) progress bar 20" id="10016" customizedId="AMSA-amsa-10016-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="AMSA (.amsa) progress bar 19" id="10016" customizedId="AMSA-amsa-10016-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="20" />
+ <property name="percentValue" type="int" value="19" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="Jalview Annotations (.annotations, .jvannotations) progress bar 24" id="10019" customizedId="Jalview Annotations-annotations,jvannotations-10019-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Annotations (.annotations, .jvannotations) progress bar 23" id="10019" customizedId="Jalview Annotations-annotations,jvannotations-10019-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="24" />
+ <property name="percentValue" type="int" value="23" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="BioJSON (.biojson) progress bar 28" id="10022" customizedId="BioJSON-biojson-10022-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="BioJSON (.biojson) progress bar 26" id="10022" customizedId="BioJSON-biojson-10022-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="28" />
+ <property name="percentValue" type="int" value="26" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="BLC (.blc) progress bar 32" id="10025" customizedId="BLC-blc-10025-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="BLC (.blc) progress bar 30" id="10025" customizedId="BLC-blc-10025-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="32" />
+ <property name="percentValue" type="int" value="30" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="Clustal (.aln) progress bar 36" id="10028" customizedId="Clustal-aln-10028-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Clustal (.aln) progress bar 34" id="10028" customizedId="Clustal-aln-10028-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="36" />
+ <property name="percentValue" type="int" value="34" />
</serializedBean>
</action>
</action>
<!-- END -->
-<!-- ENA Flatfile (.txt) BEGIN -->
- <action name="ENA Flatfile (.txt) message" id="10030" customizedId="ENA Flatfile-txt-10030-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+<!-- Fasta (.fa, .fasta) BEGIN -->
+ <action name="Fasta (.fa, .fasta) message" id="10030" customizedId="Fasta-fa,fasta-10030-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="detailMessage" type="string">ENA Flatfile (.txt)</property>
+ <property name="detailMessage" type="string">Fasta (.fa, .fasta)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
<property name="useDetail" type="boolean" value="true" />
<property name="useStatus" type="boolean" value="true" />
</serializedBean>
</action>
- <action name="ENA Flatfile (.txt) progress bar 40" id="10031" customizedId="ENA Flatfile-txt-10031-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Fasta (.fa, .fasta) progress bar 38" id="10031" customizedId="Fasta-fa,fasta-10031-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="40" />
+ <property name="percentValue" type="int" value="38" />
</serializedBean>
</action>
- <action name="ENA Flatfile (.txt) file association" id="10032" customizedId="ENA Flatfile-txt-10032-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .txt file association">
+ <action name="Fasta (.fa, .fasta) file association" id="10032" customizedId="Fasta-fa,fasta-10032-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fa,fasta file association">
<serializedBean>
- <property name="description" type="string">ENA Flatfile File</property>
- <property name="extension" type="string">txt</property>
+ <property name="description" type="string">Fasta File</property>
+ <property name="extension" type="string">fa,fasta</property>
<property name="launcherId" type="string">JALVIEW</property>
<!--<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.png</string>
</object>
</property>
- <property name="unixMimeType" type="string">application/x-embl+txt</property>
+ <property name="unixMimeType" type="string">application/x-fasta+txt</property>
<property name="windowsIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.ico</string>
</action>
<!-- END -->
-<!-- Fasta (.fa, .fasta) BEGIN -->
- <action name="Fasta (.fa, .fasta) message" id="10033" customizedId="Fasta-fa,fasta-10033-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+<!-- Jalview Features (.features, .jvfeatures) BEGIN -->
+ <action name="Jalview Features (.features, .jvfeatures) message" id="10033" customizedId="Jalview Features-features,jvfeatures-10033-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="detailMessage" type="string">Fasta (.fa, .fasta)</property>
+ <property name="detailMessage" type="string">Jalview Features (.features, .jvfeatures)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
<property name="useDetail" type="boolean" value="true" />
<property name="useStatus" type="boolean" value="true" />
</serializedBean>
</action>
- <action name="Fasta (.fa, .fasta) progress bar 44" id="10034" customizedId="Fasta-fa,fasta-10034-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Features (.features, .jvfeatures) progress bar 42" id="10034" customizedId="Jalview Features-features,jvfeatures-10034-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="44" />
+ <property name="percentValue" type="int" value="42" />
</serializedBean>
</action>
- <action name="Fasta (.fa, .fasta) file association" id="10035" customizedId="Fasta-fa,fasta-10035-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fa,fasta file association">
+ <action name="Jalview Features (.features, .jvfeatures) file association" id="10035" customizedId="Jalview Features-features,jvfeatures-10035-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .features,jvfeatures file association">
<serializedBean>
- <property name="description" type="string">Fasta File</property>
- <property name="extension" type="string">fa,fasta</property>
+ <property name="description" type="string">Jalview Features File</property>
+ <property name="extension" type="string">features,jvfeatures</property>
<property name="launcherId" type="string">JALVIEW</property>
<!--<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.png</string>
</object>
</property>
- <property name="unixMimeType" type="string">application/x-fasta+txt</property>
+ <property name="unixMimeType" type="string">application/x-jalview-features+text</property>
<property name="windowsIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.ico</string>
</action>
<!-- END -->
-<!-- Jalview Features (.features, .jvfeatures) BEGIN -->
- <action name="Jalview Features (.features, .jvfeatures) message" id="10036" customizedId="Jalview Features-features,jvfeatures-10036-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+<!-- Jalview Feature Settings File (.fc) BEGIN -->
+ <action name="Jalview Feature Settings File (.fc) message" id="10036" customizedId="Jalview Feature Settings File-fc-10036-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="detailMessage" type="string">Jalview Features (.features, .jvfeatures)</property>
+ <property name="detailMessage" type="string">Jalview Feature Settings File (.fc)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
<property name="useDetail" type="boolean" value="true" />
<property name="useStatus" type="boolean" value="true" />
</serializedBean>
</action>
- <action name="Jalview Features (.features, .jvfeatures) progress bar 48" id="10037" customizedId="Jalview Features-features,jvfeatures-10037-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Feature Settings File (.fc) progress bar 46" id="10037" customizedId="Jalview Feature Settings File-fc-10037-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="48" />
+ <property name="percentValue" type="int" value="46" />
</serializedBean>
</action>
- <action name="Jalview Features (.features, .jvfeatures) file association" id="10038" customizedId="Jalview Features-features,jvfeatures-10038-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .features,jvfeatures file association">
+ <action name="Jalview Feature Settings File (.fc) file association" id="10038" customizedId="Jalview Feature Settings File-fc-10038-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fc file association">
<serializedBean>
- <property name="description" type="string">Jalview Features File</property>
- <property name="extension" type="string">features,jvfeatures</property>
+ <property name="description" type="string">Jalview Feature Settings File File</property>
+ <property name="extension" type="string">fc</property>
<property name="launcherId" type="string">JALVIEW</property>
<!--<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.png</string>
</object>
</property>
- <property name="unixMimeType" type="string">application/x-jalview-features+text</property>
+ <property name="unixMimeType" type="string">application/x-featuresettings+txt</property>
<property name="windowsIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.ico</string>
</serializedBean>
</action>
- <action name="GenBank Flatfile (.gb, .gbk) progress bar 52" id="10040" customizedId="GenBank Flatfile-gb,gbk-10040-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="GenBank Flatfile (.gb, .gbk) progress bar 50" id="10040" customizedId="GenBank Flatfile-gb,gbk-10040-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="52" />
+ <property name="percentValue" type="int" value="50" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="Generic Features Format v2 (.gff2) progress bar 56" id="10043" customizedId="Generic Features Format v2-gff2-10043-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Generic Features Format v2 (.gff2) progress bar 53" id="10043" customizedId="Generic Features Format v2-gff2-10043-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="56" />
+ <property name="percentValue" type="int" value="53" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="Generic Features Format v3 (.gff3) progress bar 60" id="10046" customizedId="Generic Features Format v3-gff3-10046-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Generic Features Format v3 (.gff3) progress bar 57" id="10046" customizedId="Generic Features Format v3-gff3-10046-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="60" />
+ <property name="percentValue" type="int" value="57" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="JnetFile (.concise, .jnet) progress bar 64" id="10049" customizedId="JnetFile-concise,jnet-10049-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="JnetFile (.concise, .jnet) progress bar 61" id="10049" customizedId="JnetFile-concise,jnet-10049-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="64" />
+ <property name="percentValue" type="int" value="61" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="MSF (.msf) progress bar 68" id="10052" customizedId="MSF-msf-10052-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="MSF (.msf) progress bar 65" id="10052" customizedId="MSF-msf-10052-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="68" />
+ <property name="percentValue" type="int" value="65" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="PFAM (.pfam) progress bar 72" id="10055" customizedId="PFAM-pfam-10055-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PFAM (.pfam) progress bar 69" id="10055" customizedId="PFAM-pfam-10055-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="72" />
+ <property name="percentValue" type="int" value="69" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="PHYLIP (.phy) progress bar 76" id="10058" customizedId="PHYLIP-phy-10058-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PHYLIP (.phy) progress bar 73" id="10058" customizedId="PHYLIP-phy-10058-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="76" />
+ <property name="percentValue" type="int" value="73" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="PileUp (.pileup) progress bar 80" id="10061" customizedId="PileUp-pileup-10061-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PileUp (.pileup) progress bar 76" id="10061" customizedId="PileUp-pileup-10061-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="80" />
+ <property name="percentValue" type="int" value="76" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="PIR (.pir) progress bar 84" id="10064" customizedId="PIR-pir-10064-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PIR (.pir) progress bar 80" id="10064" customizedId="PIR-pir-10064-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="84" />
+ <property name="percentValue" type="int" value="80" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="RNAML (.rnaml) progress bar 88" id="10067" customizedId="RNAML-rnaml-10067-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="RNAML (.rnaml) progress bar 84" id="10067" customizedId="RNAML-rnaml-10067-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="88" />
+ <property name="percentValue" type="int" value="84" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="Substitution Matrix (.mat) progress bar 92" id="10070" customizedId="Substitution Matrix-mat-10070-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Substitution Matrix (.mat) progress bar 88" id="10070" customizedId="Substitution Matrix-mat-10070-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="92" />
+ <property name="percentValue" type="int" value="88" />
</serializedBean>
</action>
</serializedBean>
</action>
- <action name="Stockholm (.stk, .sto) progress bar 96" id="10073" customizedId="Stockholm-stk,sto-10073-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Stockholm (.stk, .sto) progress bar 92" id="10073" customizedId="Stockholm-stk,sto-10073-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="96" />
+ <property name="percentValue" type="int" value="92" />
</serializedBean>
</action>
<?xml version="1.0" encoding="UTF-8"?>
-<install4j version="10.0.6" transformSequenceNumber="10">
+<install4j version="10.0.7" transformSequenceNumber="10">
<directoryPresets config="bin/Jalview" />
<application name="${compiler:JALVIEW_APPLICATION_NAME}" applicationId="${compiler:WINDOWS_APPLICATION_ID}" mediaDir="${compiler:BUILD_DIR}" lzmaCompression="true" shortName="${compiler:INTERNAL_ID}" publisher="University of Dundee" publisherWeb="https://www.jalview.org/" version="${compiler:JALVIEW_VERSION}" allPathsRelative="true" macVolumeId="5aac4968c304f65" javaMinVersion="${compiler:JAVA_MIN_VERSION}" javaMaxVersion="${compiler:JAVA_MAX_VERSION}" allowBetaVM="true" jdkMode="jdk" jdkName="JDK 11.0">
<searchSequence>
<variable name="BACKGROUND" value="utils/channels/release/images/jalview_logo_background_fade-640x480.png" />
<variable name="BATCH_WRAPPER_SCRIPT" value="jalview.bat" />
<variable name="POWERSHELL_WRAPPER_SCRIPT" value="jalview.ps1" />
+ <variable name="WIZARD_WIDTH" value="640" description="Default/initial width of installer wizard window. Linux media types adapt this.
NOT USED" />
+ <variable name="WIZARD_HEIGHT" value="480" description="Default/initial width of installer wizard window. Linux media types adapt this.
NOT USED" />
</variables>
<codeSigning macEnabled="true" macPkcs12File="${compiler:OSX_KEYSTORE}" macNotarize="true" appleId="${compiler:OSX_APPLEID}">
<macAdditionalBinaries>
<macStaticAssociations>
<urlHandler scheme="jalview" />
<urlHandler scheme="jalviews" />
+ <urlHandler scheme="jalviewhttp" />
+ <urlHandler scheme="jalviewhttps" />
<urlHandler scheme="${compiler:EXTRA_SCHEME}" />
</macStaticAssociations>
</launcher>
<applications>
<application id="installer" beanClass="com.install4j.runtime.beans.applications.InstallerApplication" styleId="35" customIcnsFile="${compiler:JALVIEW_DIR}/${compiler:MAC_ICONS_FILE}" customIcoFile="${compiler:JALVIEW_DIR}/${compiler:WINDOWS_ICONS_FILE}">
<serializedBean>
+ <property name="frameHeight" type="int" value="480" />
+ <property name="frameWidth" type="int" value="640" />
<property name="useCustomIcon" type="boolean" value="true" />
</serializedBean>
<styleOverrides>
</group>
<action id="2350" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="launcherId" type="string">JALVIEW</property>
+ <property name="launcherId" type="string">737</property>
<property name="scheme" type="string">jalview</property>
</serializedBean>
</action>
- <action id="2450" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <action id="2822" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="launcherId" type="string">JALVIEW</property>
+ <property name="launcherId" type="string">737</property>
<property name="scheme" type="string">jalviews</property>
</serializedBean>
</action>
+ <action id="2819" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">737</property>
+ <property name="scheme" type="string">jalviewhttp</property>
+ </serializedBean>
+ </action>
+ <action id="2820" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">737</property>
+ <property name="scheme" type="string">jalviewhttps</property>
+ </serializedBean>
+ </action>
<action id="2641" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
<property name="launcherId" type="string">JALVIEW</property>
<entry filesetId="2801" />
<entry filesetId="2803" />
</exclude>
+ <variables>
+ <variable name="variable" value="720" />
+ <variable name="WIZARD_HEIGHT" value="540" />
+ </variables>
<jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
</unixInstaller>
<unixInstaller name="Linux aarch64 Shell Installer" id="2782" customizedId="LINUX-AARCH64-SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux-aarch64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
<entry filesetId="2801" />
<entry filesetId="2803" />
</exclude>
+ <variables>
+ <variable name="variable" value="720" />
+ <variable name="WIZARD_HEIGHT" value="540" />
+ </variables>
<jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_AARCH64_JAVA_VM_TGZ}" manualJreEntry="true" />
</unixInstaller>
<unixArchive name="Unix .tar.gz Archive" id="1596" customizedId="UNIX--TGZ" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}">
git://source.jalview.org / jalview.git / commitdiff