-Jalview Readme
---------------
+Please see doc/building.md for up to date build and running instructions for the Java desktop application.
-
-The source is available as a tar file and comes complete with the GNU General Public License.
-
-To build the application you will need a J2SDK 1.7+.
-
-An Ant build file (build.xml) is provided, you will need to install Apache Ant first.
-Run ant to view usage which will display a list of useful build targets.
-
-Jalview is primarily developed with eclipse, and a .project file is provided to simplify importing the source into your own eclipse workspace. A NetBeans nbbuild.xml file is also provided for developing Jalview with NetBeans - but this is not officially supported.
-
-You may also be able to use Borland JBuilder to build Jalview. A JBuilder project file
-(JalviewX.jpx, JalviewApplet.jpx) for both application and applet is provided,
-but the library dependencies are almost certainly out of date. See the build.xml
-for current dependencies.
-
-##
-
-Jalview-JS
-
-To enable transpilation of Jalview's code:
-
-1. Locate the 'dropins' directory in your eclipse installation and copy swingjs/net.sf.j2s.core.jar to it.
- - typically it is at the top of the Eclipse installation, or on OSX under Eclipse.app/Contents/Eclipse
-
-2. Restart Eclipse
-
-3. If all is well you should see the 'Java2Script' builder is listed as the primary builder for the Jalview project.
- if not, this is because your properties file needs to have the standard java builder replaced with the following:
- <name>net.sf.j2s.core.java2scriptbuilder</name>
-
-- otherwise Javascript files will now be generated in the site/swingjs/j2s directory whenever a build occurs
-
-4. Execute the 'unzip-to-site' task (if it isn't automatically run) to update the site directory with the latest versions of SwingJS, varna-js, JSmol and other dependencies required by Jalview.
-
-
-
-
-
-##
-
-For more help, read the file doc/building.html
-
-
-##################
-
-To run application...
-[ NOTE: when using the -classpath option with the '*' wildcard, the argument must be quoted to avoid shell expansion of the wildcard,
- ALSO, the wildcard MUST be as DIR/* and not DIR/*.jar etc or it will not be interpreted correctly ]
-
-on Windows use:
- java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
-and on MacOS or Linux:
- java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
-
-Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If building from source:
-
- java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview
-
-
-##################
-
-
-If you use a proxy server add
-
--Dhttp.proxyServer=YOUR.SERVER -Dhttp.proxyPort=YOURPORT
-
-If the proxy server requires authentication, add
-
--Dhttp.proxyUser=USERNAME -Dhttp.proxyPassword=PASSWORD
+JalviewJS.
+See README_GRADLE_JALVIEWJS-2019-10-22.md for build instructions for JalviewJS.
+This is a little sparse but enough to do the transpilation.
install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
install4jInstallerName = "${jalview_name} Non-Release Installer"
- install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
+ install4jExecutableName = install4j_executable_name
install4jExtraScheme = "jalviewx"
install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
.replaceAll("_*-_*", "-") // collapse _-_
.toLowerCase()
+ getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
//getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
- def errFOS = outFOS
standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
outFOS,
- standardOutput)
+ System.out)
errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
outFOS,
- errorOutput)
+ System.err)
inputs.dir(helpBuildDir)
outputs.file(helpLinksCheckerOutFile)
into getdownResourceDir
}
}
+
+ def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+ getdownWrapperScripts.each{ script ->
+ def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
+ if (s.exists()) {
+ copy {
+ from s
+ into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}"
+ }
+ getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n"
+ }
+ }
def codeFiles = []
fileTree(file(package_dir)).each{ f ->
'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
'MACOS_DMG_DS_STORE': install4jDMGDSStore,
'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+ 'WRAPPER_LINK': getdownWrapperLink,
+ 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
+ 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+ 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
'INSTALLER_NAME': install4jInstallerName,
'INSTALL4J_UTILS_DIR': install4j_utils_dir,
'GETDOWN_WEBSITE_DIR': getdown_website_dir,
println("Using projectFile "+projectFile)
if (!disableNotarization) { println("Will notarize OSX App DMG") }
}
- verbose=true
+ //verbose=true
inputs.dir(getdownWebsiteDir)
inputs.file(install4jConfFile)
new org.apache.tools.ant.util.TeeOutputStream(
logOutFOS,
stdout),
- standardOutput)
+ System.out)
errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
new org.apache.tools.ant.util.TeeOutputStream(
logErrFOS,
stderr),
- errorOutput)
+ System.err)
} else {
standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
logOutFOS,
def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
doLast {
- SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
+ def factory
+ try {
+ def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
+ factory = f.newInstance()
+ } catch (ClassNotFoundException e) {
+ throw new GradleException("Unable to create SimpleHttpFileServerFactory")
+ }
def port = Integer.valueOf(jalviewjs_server_port)
def start = port
def running = false
--- /dev/null
+Jalview Readme
+--------------
+
+
+The source is available as a tar file and comes complete with the GNU General Public License.
+
+To build the application you will need a J2SDK 1.7+.
+
+An Ant build file (build.xml) is provided, you will need to install Apache Ant first.
+Run ant to view usage which will display a list of useful build targets.
+
+Jalview is primarily developed with eclipse, and a .project file is provided to simplify importing the source into your own eclipse workspace. A NetBeans nbbuild.xml file is also provided for developing Jalview with NetBeans - but this is not officially supported.
+
+You may also be able to use Borland JBuilder to build Jalview. A JBuilder project file
+(JalviewX.jpx, JalviewApplet.jpx) for both application and applet is provided,
+but the library dependencies are almost certainly out of date. See the build.xml
+for current dependencies.
+
+##
+
+Jalview-JS
+
+To enable transpilation of Jalview's code:
+
+1. Locate the 'dropins' directory in your eclipse installation and copy swingjs/net.sf.j2s.core.jar to it.
+ - typically it is at the top of the Eclipse installation, or on OSX under Eclipse.app/Contents/Eclipse
+
+2. Restart Eclipse
+
+3. If all is well you should see the 'Java2Script' builder is listed as the primary builder for the Jalview project.
+ if not, this is because your properties file needs to have the standard java builder replaced with the following:
+ <name>net.sf.j2s.core.java2scriptbuilder</name>
+
+- otherwise Javascript files will now be generated in the site/swingjs/j2s directory whenever a build occurs
+
+4. Execute the 'unzip-to-site' task (if it isn't automatically run) to update the site directory with the latest versions of SwingJS, varna-js, JSmol and other dependencies required by Jalview.
+
+
+
+
+
+##
+
+For more help, read the file doc/building.html
+
+
+##################
+
+To run application...
+[ NOTE: when using the -classpath option with the '*' wildcard, the argument must be quoted to avoid shell expansion of the wildcard,
+ ALSO, the wildcard MUST be as DIR/* and not DIR/*.jar etc or it will not be interpreted correctly ]
+
+on Windows use:
+ java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+and on MacOS or Linux:
+ java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+
+Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If building from source:
+
+ java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview
+
+
+##################
+
+
+If you use a proxy server add
+
+-Dhttp.proxyServer=YOUR.SERVER -Dhttp.proxyPort=YOURPORT
+
+If the proxy server requires authentication, add
+
+-Dhttp.proxyUser=USERNAME -Dhttp.proxyPassword=PASSWORD
install4j_installer_file_associations = file_associations_auto-install4j8.xml
#install4j_DMG_uninstaller_app_files = uninstall_old_jalview_files.xml
install4j_build_dir = build/install4j
+install4j_executable_name = jalviewg
install4j_media_types = windows,macosArchive,unixArchive,unixInstaller
install4j_faster = false
install4j_application_categories = Science;Biology;Java;
install4j_background = jalview_logo_background_fade-640x480.png
install4j_dmg_background = jalview_dmg_background-NON-RELEASE.png
install4j_dmg_ds_store = jalview_dmg_DS_Store
+getdown_wrapper_script_dir = bin
+getdown_bash_wrapper_script = jalview.sh
+getdown_powershell_wrapper_script = jalview.ps1
+getdown_batch_wrapper_script = jalview.bat
OSX_KEYSTORE =
OSX_KEYPASS =
public static void loadProperties(String propsFile)
{
propertiesFile = propsFile;
+ String releasePropertiesFile = null;
+ boolean defaultProperties = false;
if (propsFile == null && !propsAreReadOnly)
{
+ String channelPrefsFilename = ChannelProperties
+ .getProperty("preferences.filename");
+ String releasePrefsFilename = ".jalview_properties";
propertiesFile = System.getProperty("user.home") + File.separatorChar
- + ".jalview_properties";
+ + channelPrefsFilename;
+ releasePropertiesFile = System.getProperty("user.home")
+ + File.separatorChar + releasePrefsFilename;
+ defaultProperties = true;
}
else
{
InputStream fis;
try
{
+ // props file provided as URL
fis = new URL(propertiesFile).openStream();
System.out.println(
"Loading jalview properties from : " + propertiesFile);
System.out.println(
"Disabling Jalview writing to user's local properties file.");
propsAreReadOnly = true;
-
} catch (Exception ex)
{
fis = null;
}
if (fis == null)
{
- fis = new FileInputStream(propertiesFile);
+ String readPropertiesFile = propertiesFile;
+ // if we're using the usual properties file and the channel properties
+ // file doesn't exist, read .jalview_properties
+ // (but we'll still save to the channel properties file).
+ if (defaultProperties && (!new File(propertiesFile).exists())
+ && (new File(releasePropertiesFile).exists()))
+ {
+ readPropertiesFile = releasePropertiesFile;
+ }
+ fis = new FileInputStream(readPropertiesFile);
}
applicationProperties.clear();
applicationProperties.load(fis);
public static int scale = 0;
+ public final static int MAX_SCALE = 8;
+
private static boolean doneInit = false;
private static boolean allowScalePropertyArg = false;
// get and use command line property values first
String setHiDPIProperty = System.getProperty(setHiDPIPropertyName);
- setHiDPI = setHiDPIProperty != null
- && setHiDPIProperty.equalsIgnoreCase("true");
+ boolean setHiDPIPropertyBool = Boolean.parseBoolean(setHiDPIProperty);
+
+ // allow -DsetHiDPI=false to turn off HiDPI scaling
+ if (setHiDPIProperty != null && !setHiDPIPropertyBool)
+ {
+ clear();
+ doneInit = true;
+ return;
+ }
+
+ setHiDPI = setHiDPIProperty != null && setHiDPIPropertyBool;
String setHiDPIScaleProperty = System
.getProperty(setHiDPIScalePropertyName);
try
{
setHiDPIScale = Integer.parseInt(setHiDPIScaleProperty);
+ // if setHiDPIScale property is validly set and setHiDPI property wasn't
+ // attempted to be set we assume setHiDPIScale to be true
+ if (setHiDPIProperty == null)
+ {
+ setHiDPI = true;
+ }
} catch (NumberFormatException e)
{
System.err.println(setHiDPIScalePropertyName + " property give ("
int dimensionScale = 1 + (mindimension / bigScreenThreshold);
+ // reject outrageous values -- dpiScale in particular could be mistaken
+ if (dpiScale > MAX_SCALE) {
+ dpiScale = 1;
+ }
+ if (dimensionScale > MAX_SCALE) {
+ dimensionScale = 1;
+ }
+
// choose larger of dimensionScale or dpiScale (most likely dimensionScale
// as dpiScale often misreported)
int autoScale = Math.max(dpiScale, dimensionScale);
*/
private static final String AAS = "ACDEFGHIKLMNPQRSTUVWXY";
- private static final int GAP_COUNT = 0;
+ static final int GAP_COUNT = 0;
/*
* fast lookup tables holding the index into our count
counts[offset] = (short) ++newValue;
}
}
- maxCount = Math.max(maxCount, newValue);
+
+ if (offset!=GAP_COUNT)
+ {
+ // update modal residue count
+ maxCount = Math.max(maxCount, newValue);
+ }
return newValue;
}
*/
public int addGap()
{
- int newValue;
- if (useIntCounts)
- {
- newValue = ++intCounts[GAP_COUNT];
- }
- else
- {
- newValue = ++counts[GAP_COUNT];
- }
+ int newValue = increment(GAP_COUNT);
return newValue;
}
--- /dev/null
+package jalview.fts.service.alphafold;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.util.DBRefUtils;
+import jalview.util.HttpUtils;
+import jalview.ws.dbsources.EBIAlfaFold;
+
+public class AlphafoldRestClient
+{
+
+ /**
+ * turns a uniprot ID into a fake alphafold entry for the structure chooser -
+ * fakes PDB fields in response
+ *
+ * @param UniprotID
+ * @return null or an FTS Record (if alphafold thinks it has a structure)
+ */
+ public static List<FTSData> getFTSData(// Map<String, Object> pdbJsonDoc,
+ FTSRestRequest request)
+ {
+ List<FTSData> records = new ArrayList<FTSData>();
+ String primaryKey = null;
+
+ Object[] summaryRowData;
+
+ SequenceI associatedSequence;
+
+ Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
+ SequenceI associatedSeq = request.getAssociatedSequence();
+
+ for (DBRefEntry upref : DBRefUtils
+ .selectRefs(associatedSeq.getPrimaryDBRefs(), new String[]
+ { DBRefSource.UNIPROT }))
+ {
+ String alphaFoldId = "AF-" + upref.getAccessionId() + "-F1";
+ try
+ {
+ String urls = EBIAlfaFold.getAlphaFoldCifDownloadUrl(alphaFoldId);
+ URL url = new URL(urls);
+ if (!HttpUtils.checkUrlAvailable(url, 50))
+ {
+ continue;
+ }
+ } catch (Exception mfe)
+ {
+ jalview.bin.Cache.log.debug("Exception accessing urls", mfe);
+ continue;
+ }
+ int colCounter = 0;
+ summaryRowData = new Object[(associatedSeq != null)
+ ? diplayFields.size() + 1
+ : diplayFields.size()];
+ if (associatedSeq != null)
+ {
+ associatedSequence = associatedSeq;
+ summaryRowData[0] = associatedSequence;
+ colCounter = 1;
+ }
+
+ for (FTSDataColumnI field : diplayFields)
+ {
+ String fieldData = "alphafold";// (pdbJsonDoc.get(field.getCode()) ==
+ // null) ? ""
+ // : pdbJsonDoc.get(field.getCode()).toString();
+ if (field.isPrimaryKeyColumn())
+ {
+ primaryKey = alphaFoldId;
+ summaryRowData[colCounter++] = alphaFoldId;
+ }
+ else if (fieldData == null || fieldData.isEmpty())
+ {
+ summaryRowData[colCounter++] = null;
+ }
+ else
+ {
+ try
+ {
+ summaryRowData[colCounter++] = (field.getDataType()
+ .getDataTypeClass() == Integer.class)
+ ? 1
+ : (field.getDataType()
+ .getDataTypeClass() == Double.class)
+ ? 1.3131313
+ : "AlphaFold clarity";
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.out.println("offending value:" + fieldData);
+ }
+ }
+ }
+
+ final String primaryKey1 = primaryKey;
+
+ final Object[] summaryRowData1 = summaryRowData;
+ records.add(new FTSData()
+ {
+ @Override
+ public Object[] getSummaryData()
+ {
+ return summaryRowData1;
+ }
+
+ @Override
+ public Object getPrimaryKey()
+ {
+ return primaryKey1;
+ }
+
+ /**
+ * Returns a string representation of this object;
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder summaryFieldValues = new StringBuilder();
+ for (Object summaryField : summaryRowData1)
+ {
+ summaryFieldValues.append(
+ summaryField == null ? " " : summaryField.toString())
+ .append("\t");
+ }
+ return summaryFieldValues.toString();
+ }
+
+ /**
+ * Returns hash code value for this object
+ */
+ @Override
+ public int hashCode()
+ {
+ return Objects.hash(primaryKey1, this.toString());
+ }
+
+ @Override
+ public boolean equals(Object that)
+ {
+ return this.toString().equals(that.toString());
+ }
+ });
+ }
+ return records;
+ }
+}
import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.alphafold.AlphafoldRestClient;
import jalview.util.JSONUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
.get("QTime").toString();
int numFound = Integer
.valueOf(pdbResponse.get("numFound").toString());
+ List<Object> docs = (List<Object>) pdbResponse.get("docs");
+ // add in any alphafold bits at the top
+ result = AlphafoldRestClient.getFTSData(pdbRestRequest);
if (numFound > 0)
{
- result = new ArrayList<>();
- List<Object> docs = (List<Object>) pdbResponse.get("docs");
+
for (Iterator<Object> docIter = docs.iterator(); docIter
.hasNext();)
{
Map<String, Object> doc = (Map<String, Object>) docIter.next();
result.add(getFTSData(doc, pdbRestRequest));
}
- searchResult.setNumberOfItemsFound(numFound);
- searchResult.setResponseTime(queryTime);
- searchResult.setSearchSummary(result);
}
+ searchResult.setNumberOfItemsFound(result.size());
+ searchResult.setResponseTime(queryTime);
+ searchResult.setSearchSummary(result);
+
} catch (ParseException e)
{
e.printStackTrace();
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.ws.dbsources.EBIAlfaFold;
import jalview.ws.dbsources.Pdb;
public class AppJmol extends StructureViewerBase
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
Pdb pdbclient = new Pdb();
+ EBIAlfaFold afclient = new EBIAlfaFold();
+
for (int pi = 0; pi < jmb.getPdbCount(); pi++)
{
String file = jmb.getPdbEntry(pi).getFile();
{ pdbid }), hdl);
try
{
- pdbseq = pdbclient.getSequenceRecords(pdbid);
+ if (afclient.isValidReference(pdbid))
+ {
+ pdbseq = afclient.getSequenceRecords(pdbid);
+ } else {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ }
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.structure.AtomSpec;
+import jalview.structure.StructureCommand;
import jalview.structure.StructureSelectionManager;
public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
int modelNumber = chimeraMaps.size() + 1;
String command = "setattr #" + modelNumber + " models name "
+ pe.getId();
- // FIXME reinstate this for ChimeraX 1.2, see https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4211#comment:2
- // executeCommand(new StructureCommand(command), false);
+ executeCommand(new StructureCommand(command), false);
modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
modelNumber, 0));
}
if (av.getWrapAlignment())
{
- drawWrappedPanel(gg, width, height, ranges.getStartRes());
+ drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
}
else
{
/**
* Computes the column and sequence row (and possibly annotation row when in
* wrapped mode) for the given mouse position
+ * <p>
+ * Mouse position is not set if in wrapped mode with the cursor either between
+ * sequences, or over the left or right vertical scale.
*
* @param evt
* @return
/**
* Returns the aligned sequence position (base 0) at the mouse position, or
* the closest visible one
+ * <p>
+ * Returns -1 if in wrapped mode with the mouse over either left or right
+ * vertical scale.
*
* @param evt
* @return
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
+import jalview.ws.dbsources.EBIAlfaFold;
import jalview.ws.dbsources.Pdb;
/**
{
String filePath = null;
Pdb pdbclient = new Pdb();
+ EBIAlfaFold afclient = new EBIAlfaFold();
AlignmentI pdbseq = null;
String pdbid = processingEntry.getId();
long handle = System.currentTimeMillis()
// { pdbid }));
try
{
- pdbseq = pdbclient.getSequenceRecords(pdbid);
+ if (afclient.isValidReference(pdbid))
+ {
+ pdbseq = afclient.getSequenceRecords(pdbid);
+ } else {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ }
} catch (Exception e)
{
System.err.println(
String choice = null;
JFileChooser chooser = new JFileChooser();
+ // Enable appBundleIsTraversable in macOS FileChooser to allow selecting
+ // hidden executables within .app dirs
+ if (Platform.isMac())
+ {
+ chooser.putClientProperty("JFileChooser.appBundleIsTraversable",
+ true);
+ }
+
// chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.open_local_file"));
registerPDBFile(pdb.getId().trim(), pdbFile);
}
// if PDBId is unavailable then skip SIFTS mapping execution path
- isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-");
} catch (Exception ex)
{
defaultProps.put("uod_banner.32", "/default_images/UoD_banner-32.png");
defaultProps.put("default_appbase",
"https://www.jalview.org/getdown/release/1.8");
+ defaultProps.put("preferences.filename", ".jalview_properties");
// load channel_properties
Properties tryChannelProps = new Properties();
if (channelPropsURL == null)
{
// complete failure of channel_properties, set all properties to defaults
- System.err
- .println("Failed to find '" + CHANNEL_PROPERTIES_FILENAME
- + "' file at '"
- + (channelPropsURL == null ? "null"
- : channelPropsURL.toString())
- + "'. Using class defaultProps.");
+ System.err.println("Failed to find '" + CHANNEL_PROPERTIES_FILENAME
+ + "' file at '"
+ + (channelPropsURL == null ? "null"
+ : channelPropsURL.toString())
+ + "'. Using class defaultProps.");
tryChannelProps = defaultProps;
}
else
import java.io.IOException;
import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.ProtocolException;
import java.net.URL;
+import java.util.List;
+
+import javax.ws.rs.HttpMethod;
public class HttpUtils
{
{
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
+ {
+ // System.out.println(System.currentTimeMillis() + " " + url);
+
+ HttpURLConnection connection = (HttpURLConnection) url.openConnection();
+
+ connection.setRequestMethod(HttpMethod.HEAD);
+
+ connection.setDoInput(true);
+
+ connection.setUseCaches(false);
+ connection.setConnectTimeout(300);
+ connection.setReadTimeout(readTimeout);
+ return connection.getResponseCode() == 200;
+ }
}
--- /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.ws.dbsources;
+
+import jalview.api.FeatureSettingsModelI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FormatAdapter;
+import jalview.io.PDBFeatureSettings;
+import jalview.structure.StructureImportSettings;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
+import jalview.ws.utils.UrlDownloadClient;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * @author JimP
+ *
+ */
+public class EBIAlfaFold extends EbiFileRetrievedProxy
+{
+ private static final String SEPARATOR = "|";
+
+ private static final String COLON = ":";
+
+ private static final int PDB_ID_LENGTH = 4;
+
+ public EBIAlfaFold()
+ {
+ super();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+ */
+ @Override
+ public String getAccessionSeparator()
+ {
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+ */
+ @Override
+ public Regex getAccessionValidator()
+ {
+ return new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSource()
+ */
+ @Override
+ public String getDbSource()
+ {
+ return "ALPHAFOLD";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbVersion()
+ */
+ @Override
+ public String getDbVersion()
+ {
+ return "1";
+ }
+ public static String getAlphaFoldCifDownloadUrl(String id)
+ {
+ return "https://alphafold.ebi.ac.uk/files/"+id+"-model_v1.cif";
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+ */
+ @Override
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ AlignmentI pdbAlignment = null;
+ String chain = null;
+ String id = null;
+ if (queries.indexOf(COLON) > -1)
+ {
+ chain = queries.substring(queries.indexOf(COLON) + 1);
+ id = queries.substring(0, queries.indexOf(COLON));
+ }
+ else
+ {
+ id = queries;
+ }
+
+ if (!isValidReference(id))
+ {
+ System.err.println("(AFClient) Ignoring invalid pdb query: '" + id + "'");
+ stopQuery();
+ return null;
+ }
+ String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
+
+ try {
+ File tmpFile = File.createTempFile(id,"cif");
+ UrlDownloadClient.download(alphaFoldCif, tmpFile);
+ file = tmpFile.getAbsolutePath();
+ if (file == null)
+ {
+ return null;
+ }
+ // todo get rid of Type and use FileFormatI instead?
+ FileFormatI fileFormat = FileFormat.MMCif;
+ pdbAlignment = new FormatAdapter().readFile(tmpFile, DataSourceType.FILE,
+ fileFormat);
+ if (pdbAlignment != null)
+ {
+ List<SequenceI> toremove = new ArrayList<SequenceI>();
+ for (SequenceI pdbcs : pdbAlignment.getSequences())
+ {
+ String chid = null;
+ // Mapping map=null;
+ for (PDBEntry pid : pdbcs.getAllPDBEntries())
+ {
+ if (pid.getFile() == file)
+ {
+ chid = pid.getChainCode();
+
+ }
+ }
+ if (chain == null || (chid != null && (chid.equals(chain)
+ || chid.trim().equals(chain.trim())
+ || (chain.trim().length() == 0 && chid.equals("_")))))
+ {
+ // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
+ // TODO: suggest simplify naming to 1qip|A as default name defined
+ pdbcs.setName(id
+ + SEPARATOR + pdbcs.getName());
+ // Might need to add more metadata to the PDBEntry object
+ // like below
+ /*
+ * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
+ * entry.setId(id); if (entry.getProperty() == null)
+ * entry.setProperty(new Hashtable());
+ * entry.getProperty().put("chains", pdbchain.id + "=" +
+ * sq.getStart() + "-" + sq.getEnd());
+ * sq.getDatasetSequence().addPDBId(entry);
+ */
+ // Add PDB DB Refs
+ // We make a DBRefEtntry because we have obtained the PDB file from
+ // a
+ // verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+ // information
+ DBRefEntry dbentry = new DBRefEntry(getDbSource(),
+ getDbVersion(), (chid == null ? id : id + chid));
+ // dbentry.setMap()
+ pdbcs.addDBRef(dbentry);
+ }
+ else
+ {
+ // mark this sequence to be removed from the alignment
+ // - since it's not from the right chain
+ toremove.add(pdbcs);
+ }
+ }
+ // now remove marked sequences
+ for (SequenceI pdbcs : toremove)
+ {
+ pdbAlignment.deleteSequence(pdbcs);
+ if (pdbcs.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : pdbcs.getAnnotation())
+ {
+ pdbAlignment.deleteAnnotation(aa);
+ }
+ }
+ }
+ }
+
+ if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
+ {
+ throw new Exception(MessageManager.formatMessage(
+ "exception.no_pdb_records_for_chain", new String[]
+ { id, ((chain == null) ? "' '" : chain) }));
+ }
+
+ } catch (Exception ex) // Problem parsing PDB file
+ {
+ stopQuery();
+ throw (ex);
+ }
+ return pdbAlignment;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+ */
+ @Override
+ public boolean isValidReference(String accession)
+ {
+ Regex r = getAccessionValidator();
+ return r.search(accession.trim());
+ }
+
+ /**
+ * human glyoxalase
+ */
+ @Override
+ public String getTestQuery()
+ {
+ return "1QIP";
+ }
+
+ @Override
+ public String getDbName()
+ {
+ return "PDB"; // getDbSource();
+ }
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
+
+ /**
+ * Returns a descriptor for suitable feature display settings with
+ * <ul>
+ * <li>ResNums or insertions features visible</li>
+ * <li>insertions features coloured red</li>
+ * <li>ResNum features coloured by label</li>
+ * <li>Insertions displayed above (on top of) ResNums</li>
+ * </ul>
+ */
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return new PDBFeatureSettings();
+ }
+}
assertEquals(rc.getCount('.'), 4);
assertFalse(rc.isUsingOtherData());
assertFalse(rc.isCountingInts());
+
+ rc.set(ResidueCount.GAP_COUNT, Short.MAX_VALUE-2);
+ assertEquals(rc.getGapCount(), Short.MAX_VALUE-2);
+ assertFalse(rc.isCountingInts());
+ rc.addGap();
+ assertEquals(rc.getGapCount(), Short.MAX_VALUE-1);
+ assertFalse(rc.isCountingInts());
+ rc.addGap();
+ assertEquals(rc.getGapCount(), Short.MAX_VALUE);
+ rc.addGap();
+ assertTrue(rc.isCountingInts());
+ assertEquals(rc.getGapCount(), Short.MAX_VALUE+1);
}
@Test(groups = "Functional")
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
+import java.awt.EventQueue;
+import java.awt.FontMetrics;
+import java.awt.event.MouseEvent;
+import java.lang.reflect.InvocationTargetException;
+
+import javax.swing.JLabel;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.SeqPanel.MousePos;
import jalview.io.FileLoader;
import jalview.util.MessageManager;
import jalview.viewmodel.ViewportRanges;
-
-import java.awt.EventQueue;
-import java.awt.event.MouseEvent;
-import java.lang.reflect.InvocationTargetException;
-
-import javax.swing.JLabel;
-
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
import junit.extensions.PA;
public class SeqPanelTest
{
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "false");
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+ Cache.applicationProperties.setProperty("FONT_SIZE", "10");
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
AlignViewportI av = alignFrame.getViewport();
e.printStackTrace();
}
}
+ @Test(groups = "Functional")
+ public void testFindMousePosition_wrapped_scales_longSequence()
+ {
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "false");
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+ Cache.applicationProperties.setProperty("FONT_SIZE", "14");
+ Cache.applicationProperties.setProperty("FONT_NAME", "SansSerif");
+ Cache.applicationProperties.setProperty("FONT_STYLE", "0");
+ // sequence of 50 bases, doubled 10 times, = 51200 bases
+ String dna = "ATGGCCATTGGGCCCAAATTTCCCAAAGGGTTTCCCTGAGGTCAGTCAGA";
+ for (int i = 0 ; i < 10 ; i++)
+ {
+ dna += dna;
+ }
+ assertEquals(dna.length(), 51200);
+ AlignFrame alignFrame = new FileLoader()
+ .LoadFileWaitTillLoaded(dna, DataSourceType.PASTE);
+ SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
+ AlignViewport av = alignFrame.getViewport();
+ av.setScaleAboveWrapped(true);
+ av.setScaleLeftWrapped(true);
+ av.setScaleRightWrapped(true);
+ alignFrame.alignPanel.updateLayout();
+
+ try
+ {
+ Thread.sleep(200);
+ } catch (InterruptedException e)
+ {
+ }
+
+ final int charHeight = av.getCharHeight();
+ final int charWidth = av.getCharWidth();
+ assertEquals(charHeight, 17);
+ assertEquals(charWidth, 12);
+
+ FontMetrics fm = testee.getFontMetrics(av.getFont());
+ int labelWidth = fm.stringWidth("00000") + charWidth;
+ assertEquals(labelWidth, 57); // 5 x 9 + charWidth
+ assertEquals(testee.seqCanvas.getLabelWidthWest(), labelWidth);
+
+ int x = 0;
+ int y = 0;
+
+ /*
+ * mouse at top left of wrapped panel; there is a gap of 2 * charHeight
+ * above the alignment
+ */
+ MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y,
+ 0, 0, 0, false, 0);
+ MousePos pos = testee.findMousePosition(evt);
+ assertEquals(pos.column, -1); // over scale left, not an alignment column
+ assertEquals(pos.seqIndex, -1); // above sequences
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor over scale above first sequence
+ */
+ y += charHeight;
+ x = labelWidth;
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.column, 0);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor over scale left of first sequence
+ */
+ y += charHeight;
+ x = 0;
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.column, -1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor over start of first sequence
+ */
+ x = labelWidth;
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.column, 0);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * move one character right, to bottom pixel of same row
+ */
+ x += charWidth;
+ y += charHeight - 1;
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.column, 1);
+
+ /*
+ * move down one pixel - now in the no man's land between rows
+ */
+ y += 1;
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.column, 1);
+
+ /*
+ * move down two char heights less one pixel - still in the no man's land
+ * (scale above + spacer line)
+ */
+ y += (2 * charHeight - 1);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.column, 1);
+
+ /*
+ * move down one more pixel - now on the next row of the sequence
+ */
+ y += 1;
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.column, 1 + av.getWrappedWidth());
+
+ /*
+ * scroll to near the end of the sequence
+ */
+ SearchResultsI sr = new SearchResults();
+ int scrollTo = dna.length() - 1000;
+ sr.addResult(av.getAlignment().getSequenceAt(0), scrollTo, scrollTo);
+ alignFrame.alignPanel.scrollToPosition(sr);
+
+ /*
+ * place the mouse on the first column of the 6th sequence, and
+ * verify that (computed) findMousePosition matches (actual) ViewportRanges
+ */
+ x = labelWidth;
+ y = 17 * charHeight; // 17 = 6 times two header rows and 5 sequence rows
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ int expected = av.getRanges().getStartRes() + 5 * av.getWrappedWidth();
+ assertEquals(pos.column, expected);
+ }
}
uod_banner.30=/images/UoD_banner-30.png
uod_banner.32=/images/UoD_banner-32.png
default_appbase=https://www.jalview.org/getdown/release/1.8
+preferences.filename=.jalview_properties
uod_banner.30=/images/UoD_banner-30.png
uod_banner.32=/images/UoD_banner-32.png
default_appbase=https://www.jalview.org/getdown/develop/11
+preferences.filename=.jalview_develop_properties
uod_banner.30=/images/UoD_banner-30.png
uod_banner.32=/images/UoD_banner-32.png
default_appbase=https://www.jalview.org/getdown/release/1.8
+preferences.filename=.jalview_properties
uod_banner.30=/images/UoD_banner-30.png
uod_banner.32=/images/UoD_banner-32.png
default_appbase=https://www.jalview.org/getdown/release/1.8
+preferences.filename=.jalview_properties
uod_banner.30=/images/UoD_banner-30.png
uod_banner.32=/images/UoD_banner-32.png
default_appbase=https://www.jalview.org/getdown/release/1.8
+preferences.filename=.jalview_properties
--- /dev/null
+@ECHO OFF
+
+REM This is the Jalview batch script wrapper to run the powershell script of the same name.
+REM There is nothing specific to Jalview.
+
+REM ******************************************************************************
+REM If you need to set a full path to the PowerShell executable please do so here:
+SET PWSHPATH=
+REM ******************************************************************************
+
+REM This is some DOS magic to substitute the extension in the full path of this batch script with .ps1
+SET SCRIPTPATH=%~dpn0.ps1
+
+REM PowerShell script isn't where it should be!
+IF NOT EXIST %SCRIPTPATH% (
+ ECHO Could not find PowerShell script %SCRIPTPATH%. Is %~nx0 in the right folder?
+ EXIT /B 1
+)
+
+REM Look for either pwsh.exe or powershell.exe if not set in PWSHPATH above.
+REM pwsh.exe is preferred as it is likely to be a newer version.
+SET PWSH=
+IF DEFINED PWSHPATH (
+ SET PWSH=%PWSHPATH%
+)
+FOR %%X IN (pwsh.exe powershell.exe) DO (
+ IF NOT DEFINED PWSH (
+ IF NOT "%%~$PATH:X" == "" (
+ REM Found a PowerShell executable in the PATH
+ SET PWSH=%%X
+ GOTO end_looking
+ )
+ )
+)
+:end_looking
+
+IF NOT DEFINED PWSH (
+ REM No PowerShell executable found -- tell the user what to do.
+ ECHO No PowerShell found in %%PATH%%. If PowerShell is installed either
+ ECHO 1. add it to your PATH, or
+ ECHO 2. edit the PWSHPATH value at the top of this file:
+ ECHO "%~dpnx0"
+ ECHO.
+ ECHO %~n0 on the command line requires PowerShell. To install PowerShell see
+ ECHO https://docs.microsoft.com/en-us/powershell/scripting/install/installing-powershell
+ EXIT /B 2
+)
+
+REM Run the PowerShell script
+%PWSH% -NoProfile -ExecutionPolicy Bypass -Command "& '%SCRIPTPATH%' %*";
--- /dev/null
+#!/usr/bin/env pwsh
+
+# save args and first parameter
+$myArgs = $args.Clone()
+$myArg1 = $args[0]
+
+# setup for powershell version < 6.0
+[bool] $myIsWindows = 0
+[bool] $myIsMacOS = 0
+if ( $IsWindows -eq $null ) {
+ # for powershell version < 6.0 let's assume Windows
+ $myIsWindows = 1
+ $myIsMacOS = 0
+} else {
+ $myIsWindows = $IsWindows
+ $myIsMacOS = $IsMacOS
+}
+
+# parent dir of this actual script (which should be the getdown appdir/bin). Follow all symlinks. Like GNU readlink -f
+function Readlink-f {
+ Param($Link)
+ $Return = $null
+ $c = 0
+ $max = 100 # just in case we end up in a loop
+ [bool] $found = 0
+ $file = Get-Item -Path $Link
+ $prevfile = $null
+ While ( $c -lt $max -and "${file}" -ne "${prevfile}" -and -not $found ) {
+ $prevfile = $file
+ [string] $target = ( $file ).Target
+ If ( $target -eq $null -or ( $file ).LinkType -ne "SymbolicLink" ) {
+ $Return = $file
+ $found = 1
+ } Else {
+ If ( $( Split-Path -Path $target -IsAbsolute ) ) {
+ $file = Get-Item -Path $target
+ } Else {
+# symbolic link is relative: combine previous link parent dir with the link target and resolve
+ $file = Get-Item -Path ( Join-Path -Path ( Split-Path -Path $prevfile -Parent ) -ChildPath $target -Resolve )
+ }
+ }
+ $c++
+ }
+ if ( -not $found ) {
+ throw "Could not determine path to actual file $( Split-Path -Path $Link -Leaf )"
+ }
+ $Return
+}
+
+# Avert problem with unix version of powershell and tell user the reason (Windows must always have .ps1 extension)
+if ( $MyInvocation.MyCommand.Path -eq $null ) {
+ throw "Script or link to script must have extension .ps1"
+}
+
+
+$CMDPATH = ( Get-Item $MyInvocation.MyCommand.Path )
+$SCRIPTPATH = Readlink-f -Link $CMDPATH
+$DIR = Split-Path -Path $SCRIPTPATH -Parent
+
+# set the "-open" parameter if myArg1 is non-zero-length, and not "open" or starts with a "-"
+$OPEN = ""
+if ( $myArg1.length -gt 0 -and ( -not $myArg1.StartsWith("-") ) -and $myArg1 -cne "open" ) {
+ $OPEN = "-open"
+}
+
+$APPDIR = If ( ( Split-Path -Path $DIR -Leaf ) -eq "bin" ) { Split-Path -Path $DIR -Parent } Else { $DIR }
+$JAVAEXE = If ( $myIsWindows ) { "java.exe" } Else { "java" }
+$JAVA = Join-Path -Path $APPDIR -ChildPath ( "jre/" + $( If ( $myIsMacOS ) { "Contents/Home/" } Else { "" } ) + "bin/${JAVAEXE}" )
+$GETDOWNTXT = Join-Path -Path $APPDIR -ChildPath "getdown.txt"
+
+# look for getdown.txt -- needed to create classpath
+if ( -not ( Test-Path -Path "${GETDOWNTXT}" ) ) {
+ throw "Cannot find ${GETDOWNTXT}"
+}
+
+# look for bundled JRE. Might not be there if unix installer used in which case just invoke "java"
+if ( -not ( Test-Path -Path "${JAVA}" ) ) {
+ Write-Host "Cannot find bundled ${JAVAEXE}. Using system ${JAVAEXE} and hoping for the best!"
+ $JAVA = $JAVAEXE
+}
+
+$CLASSPATH = ( Select-String -Path "${GETDOWNTXT}" -AllMatches -Pattern "code\s*=\s*(.*)$" | foreach { Join-Path -Path $APPDIR -ChildPath $($_.Matches.Groups[1].Value ) } ) -join $( If ( $myIsWindows ) { ";" } Else { ":" } )
+
+# quote the args and the command (in case of spaces) with escape chars (`) and precede with & to indicate command not string
+$myArgsString = '"' + $($myArgs -join '" "') + '"'
+Invoke-Expression -Command "& `"${JAVA}`" -cp `"${CLASSPATH}`" jalview.bin.Launcher ${OPEN} ${myArgsString}"
+
--- /dev/null
+#!/usr/bin/env bash
+
+declare -a ARGS=("${@}")
+ARG1=$1
+
+# this whole next part is because there's no readlink -f in Darwin
+function readlinkf() {
+ FINDFILE="$1"
+ FILE="${FINDFILE}"
+ PREVFILE=""
+ C=0
+ MAX=100 # just in case we end up in a loop
+ FOUND=0
+ while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
+ PREVFILE="${FILE}"
+ FILE="$(readlink "${FILE}")"
+ if [ -z "${FILE}" ]; then
+ # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
+ FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
+ FOUND=1
+ elif [ "${FILE#/}" = "${FILE}" ]; then
+ # FILE is not an absolute path link, we need to add the relative path to the previous dir
+ FILE="$(dirname "${PREVFILE}")/${FILE}"
+ fi
+ C=$((C+1))
+ done
+ if [ "${FOUND}" -ne 1 ]; then
+ echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
+ exit 1
+ fi
+ echo "${FILE}"
+}
+
+ISMACOS=0
+if [ "$( uname -s )" = "Darwin" ]; then
+ ISMACOS=1
+fi
+
+declare -a JVMARGS=()
+
+# set vars for being inside the macos App Bundle
+if [ "${ISMACOS}" = 1 ]; then
+# MACOS ONLY
+ DIR="$(dirname "$(readlinkf "$0")")"
+ APP="${DIR%.app/Contents/*}".app
+ if [ "${APP}" = "${APP%.app}" ]; then
+ echo "Could not find Jalview.app" >&2
+ exit 2
+ fi
+ APPDIR="${APP}/Contents/Resources/app"
+ JAVA="${APPDIR}/jre/Contents/Home/bin/java"
+ JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
+else
+# NOT MACOS
+ DIR="$(dirname "$(readlink -f "$0")")"
+ APPDIR="${DIR%/bin}"
+ JAVA="${APPDIR}/jre/bin/java"
+fi
+
+SYSJAVA=java
+GETDOWNTXT="${APPDIR}/getdown.txt"
+
+CLASSPATH=""
+# save an array of JAR paths in case we're in WSL (see later)
+declare -a JARPATHS=()
+if [ -e "${GETDOWNTXT}" ]; then
+ # always check grep and sed regexes on macos -- they're not the same
+ for JAR in $(grep -e '^code\s*=\s*' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
+ [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
+ CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
+ JARPATHS=( "${JARPATHS[@]}" "${APPDIR}/${JAR}" )
+ done
+else
+ echo "Cannot find getdown.txt" >&2
+ exit 3
+fi
+
+# WINDOWS ONLY (Cygwin or WSL)
+# change paths for Cygwin or Windows Subsystem for Linux (WSL)
+if [ "${ISMACOS}" != 1 ]; then # macos doesn't like uname -o, best to avoid
+ if [ "$(uname -o)" = "Cygwin" ]; then
+ # CYGWIN
+ echo "When using relative paths in args within Cygwin, please start with './' or '../'" >&2
+ CLASSPATH=$(cygpath -pw "${CLASSPATH}")
+ # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
+ ARGS=()
+ for ARG in "${@}"; do
+ if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
+ ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" )
+ else
+ ARGS=( "${ARGS[@]}" "${ARG}" )
+ fi
+ done
+ elif uname -r | grep Microsoft >/dev/null; then
+ # WSL
+ echo "When using relative paths in args within WSL, please start with './' or '../'" >&2
+ CLASSPATH=""
+ for JARPATH in "${JARPATHS[@]}"; do
+ [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH};"
+ CLASSPATH="${CLASSPATH}$(wslpath -aw "${JARPATH}")"
+ done
+ ARGS=()
+ for ARG in "${@}"; do
+ if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
+ # annoyingly wslpath does not work if the file doesn't exist!
+ ARGBASENAME="$(basename "${ARG}")"
+ ARGDIRNAME="$(dirname "${ARG}")"
+ ARGS=( "${ARGS[@]}" "$(wslpath -aw "${ARGDIRNAME}")\\${ARGBASENAME}" )
+ else
+ ARGS=( "${ARGS[@]}" "${ARG}" )
+ fi
+ done
+ JAVA="${JAVA}.exe"
+ SYSJAVA="java.exe"
+ fi
+fi
+
+# Is there a bundled Java? If not just try one in the PATH (do need .exe in WSL)
+if [ \! -e "${JAVA}" ]; then
+ JAVA=$SYSJAVA
+ echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
+fi
+
+# check to see if $1 is set and is not start of other cli args
+OPEN=""
+if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
+ # first argument exists and does not start with a "-" and is not "open"
+ OPEN="-open"
+fi
+
+# don't quote $OPEN (don't want it accidentally mistaken as an empty string arg!)
+"${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "${ARGS[@]}"
<?xml version="1.0" encoding="UTF-8"?>
-<install4j version="8.0.10" transformSequenceNumber="8">
- <directoryPresets config="../.." />
+<install4j version="8.0.11" transformSequenceNumber="8">
+ <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="9999999999${compiler:JAVA_MAX_VERSION}" allowBetaVM="true" jdkMode="jdk" jdkName="JDK 11.0">
<searchSequence>
<directory location="${compiler:JRE_DIR}" />
<variable name="INTERNAL_ID" value="Jalview" />
<variable name="WINDOWS_APPLICATION_ID" value="6595-2347-1923-0725" />
<variable name="MACOS_DMG_DS_STORE" value="jalview_dmg_DS_Store" />
- <variable name="MACOS_DMG_BG_IMAGE" />
+ <variable name="MACOS_DMG_BG_IMAGE" value="jalview_dmg_background-72dpi.png" />
+ <variable name="WRAPPER_LINK" value="jalview" />
+ <variable name="BASH_WRAPPER_SCRIPT" value="jalview.sh" />
+ <variable name="WRAPPER_SCRIPT_BIN_DIR" value="bin" />
<variable name="INSTALLER_NAME" value="Jalview Installer" />
<variable name="INSTALL4J_UTILS_DIR" value="utils/install4j" />
<variable name="GETDOWN_WEBSITE_DIR" value="getdown/website" />
<entry>jspawnhelper</entry>
<entry>libfreetype.dylib.6</entry>
<entry>applet</entry>
+ <entry>jaotc</entry>
+ <entry>jfr</entry>
+ <entry>jrunscript</entry>
+ <entry>libjli.dylib</entry>
</macAdditionalBinaries>
</codeSigning>
</application>
</mountPoints>
<entries>
<dirEntry mountPoint="454" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_FILES_DIR}/${compiler:JAVA_VERSION}" uninstallMode="2" overrideOverwriteMode="true" overrideUninstallMode="true" subDirectory="files" />
- <dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_WEBSITE_DIR}/${compiler:JAVA_VERSION}" uninstallMode="2" overrideOverwriteMode="true" overrideUninstallMode="true" subDirectory="files" />
+ <dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_WEBSITE_DIR}/${compiler:JAVA_VERSION}" uninstallMode="2" overrideOverwriteMode="true" overrideUninstallMode="true" subDirectory="files">
+ <exclude>
+ <entry location="${compiler:WRAPPER_SCRIPT_BIN_DIR}" />
+ </exclude>
+ </dirEntry>
<dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/examples" overwriteMode="1" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="examples" />
+ <dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_WEBSITE_DIR}/${compiler:JAVA_VERSION}/${compiler:WRAPPER_SCRIPT_BIN_DIR}" fileMode="755" overrideFileMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:WRAPPER_SCRIPT_BIN_DIR}" overrideDirMode="true" />
<dirEntry mountPoint="884" file="${compiler:MACOS_JAVA_VM_DIR}" fileMode="755" overrideFileMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
<dirEntry mountPoint="885" file="${compiler:WINDOWS_JAVA_VM_DIR}" fileMode="755" overrideFileMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
<dirEntry mountPoint="1875" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_WEBSITE_DIR}/${compiler:JAVA_VERSION}/${compiler:GETDOWN_DIST_DIR}" overwriteMode="1" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:GETDOWN_DIST_DIR}" overrideDirMode="true" />
<property name="obtainIfAdminWin" type="boolean" value="false" />
</serializedBean>
</action>
+ <action name="Set unixUserBinDir (Linux or Unix)" id="2738" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="script">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">String userHome = (String)context.getVariable("sys.userHome");
+
+String[] tryPaths = new String[] {
+ "bin",
+ ".local" + File.separator + "bin",
+ "local" + File.separator + "bin",
+ "opt" + File.separator + "bin"
+};
+
+for (int i = 0; i < tryPaths.length; i++) {
+ String tryPath = tryPaths[i];
+ File unixUserBinDir = new File(userHome + File.separator + tryPath);
+ if (unixUserBinDir.exists()) {
+ return tryPath;
+ }
+}
+
+return null;
+</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">unixUserBinDir</property>
+ </serializedBean>
+ <condition>Util.isLinux() || Util.isUnixInstaller()</condition>
+ </action>
</actions>
</screen>
</startup>
</action>
<action id="2542" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="statusMessage" type="string">Creating file associations</property>
+ <property name="statusMessage" type="string">Finished creating file associations</property>
<property name="useDetail" type="boolean" value="true" />
<property name="useStatus" type="boolean" value="true" />
</serializedBean>
</serializedBean>
<condition>context.getBooleanVariable("addToDockAction")</condition>
</action>
+ <action name="Linux/Unix symlink" id="2733" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make symlink to wrapper script">
+ <serializedBean>
+ <property name="file">
+ <object class="java.io.File">
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}</string>
+ </object>
+ </property>
+ <property name="linkFile">
+ <object class="java.io.File">
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>!Util.isWindows()</condition>
+ </action>
+ <action name="Add Jalview bin to the user's path (Windows)" id="2740" beanClass="com.install4j.runtime.beans.actions.misc.ModifyEnvironmentVariableAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not add "${installer:sys.contentDir}\${compiler:WRAPPER_SCRIPT_BIN_DIR}" to the Path environment variable">
+ <serializedBean>
+ <property name="type" type="enum" class="com.install4j.runtime.beans.actions.misc.ModifyStringType" value="APPEND" />
+ <property name="value" type="string">${installer:sys.contentDir}\${compiler:WRAPPER_SCRIPT_BIN_DIR}</property>
+ <property name="variableName" type="string">Path</property>
+ </serializedBean>
+ <condition>context.getBooleanVariable("appendToPathAction")</condition>
+ </action>
+ <action name="Create symbolic link to jalview.sh in user's local bin" id="2739" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixUserBinDir}">
+ <serializedBean>
+ <property name="file">
+ <object class="java.io.File">
+ <string>${installer:sys.contentDir}/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}</string>
+ </object>
+ </property>
+ <property name="linkFile">
+ <object class="java.io.File">
+ <string>${installer:sys.userHome}/${installer:unixUserBinDir}/${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>context.getBooleanVariable("makeSymbolicLink") && ( Util.isLinux() || Util.isUnixInstaller() ) && ( context.getVariable("unixUserBinDir") != null )</condition>
+ </action>
</actions>
<formComponents>
<formComponent id="21" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent" insetBottom="10">
</serializedBean>
<visibilityScript>Util.isMacOS()</visibilityScript>
</formComponent>
+ <formComponent name="Add jalview bin to the user's Path environment variable (Windows)" id="2734" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent">
+ <serializedBean>
+ <property name="checkboxText" type="string">Add ${compiler:JALVIEW_APPLICATION_NAME}'s bin folder to the Path environment variable</property>
+ <property name="initiallySelected" type="boolean" value="true" />
+ <property name="variableName" type="string">appendToPathAction</property>
+ </serializedBean>
+ <visibilityScript>Util.isWindows()</visibilityScript>
+ </formComponent>
+ <formComponent name="Make a symbolic link to jalview.sh bash script in the user's local bin (Linux or Unix)" id="2736" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent">
+ <serializedBean>
+ <property name="checkboxText" type="string">Make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixUserBinDir}</property>
+ <property name="initiallySelected" type="boolean" value="true" />
+ <property name="variableName" type="string">makeSymbolicLink</property>
+ </serializedBean>
+ <visibilityScript>( Util.isLinux() || Util.isUnixInstaller() ) && ( context.getVariable("unixUserBinDir") != null )</visibilityScript>
+ </formComponent>
</formComponents>
</screen>
</screens>
</action>
<action id="1525" beanClass="com.install4j.runtime.beans.actions.files.DeleteFileAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="files" type="array" class="java.io.File" length="36">
+ <property name="files" type="array" class="java.io.File" length="40">
<element index="0">
<object class="java.io.File">
<string>jre</string>
<string>build_*</string>
</object>
</element>
+ <element index="36">
+ <object class="java.io.File">
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}</string>
+ </object>
+ </element>
+ <element index="37">
+ <object class="java.io.File">
+ <string>bin</string>
+ </object>
+ </element>
+ <element index="38">
+ <object class="java.io.File">
+ <string>channel.props</string>
+ </object>
+ </element>
+ <element index="39">
+ <object class="java.io.File">
+ <string>channel.propsv</string>
+ </object>
+ </element>
</property>
<property name="recursive" type="boolean" value="true" />
</serializedBean>
<file name=".DS_Store" file="${compiler:JALVIEW_DIR}/${compiler:MACOS_DMG_DS_STORE}" />
<file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/Jalview-File.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Jalview-File.icns" />
<file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/Jalview-Launch.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Jalview-Launch.icns" />
+ <symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS/${compiler:WRAPPER_LINK}" target="../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}" />
</topLevelFiles>
</macosArchive>
<unixInstaller name="Linux x64 Shell Installer" id="1595" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux_x64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
--- /dev/null
+Signing and Notarizing install4j DMGs for OSX
+
+0. You will need an up to date Apple Developer ID subscription and have a valid developer key for signing/notarizing apps, installers and DMGs available on your system.
+
+1. Build the install4j installers - signing these for windows requires a Certum cryptokey or other suitable java codesigning cert. Details to be provided.
+
+2. Unpack the OSX installer to a local directory
+hdiutil attach build/install4j/11/Jalview_Develop-2_11_2_0dev-d20210128-macos-java_11.dmg
+mkdir newdmg; ditto /Volumes/Jalview\ Develop\ Installer newdmg/
+
+3. Remove the uninstaller if necessary/and/or others, and then deep sign the dmg
+
+xattr -cr ./newdmg/Jalview\ Develop.app/Contents/Resources/app/jre/Contents/MacOS/libjli.dylib
+codesign --verify --deep -v ./newdmg/Jalview\ Develop.app/Contents/Resources/app/jre/Contents/MacOS/libjli.dylib
+
+codesign --force --deep -vvvv -s "Developer ID" --options runtime --entitlements ./utils/osx_signing/entitlements.txt ./newdmg/Jalview\ Develop.app/Contents/Resources/app/jre/Contents/MacOS/libjli.dylib
+
+codesign --verify --deep -v ./newdmg/Jalview\ Develop.app/Contents/Resources/app/jre/Contents/MacOS/libjli.dylib
+
+codesign --force --deep -vvvv -s "Developer ID" --options runtime --entitlements ./utils/osx_signing/entitlements.txt ./newdmg/Jalview\ Develop.app/Contents/MacOS/JavaApplicationStub
+
+hdiutil create -megabytes 240 -srcfolder ./newdmg -volname 'Jalview Develop Installer (2.11.2)' Jalview_Develop-2_11_2-macos-java_11.dmg
+
+codesign --force --deep -vvvv -s "Developer ID" --options runtime --entitlements ./utils/osx_signing/entitlements.txt Jalview_Develop-2_11_2-macos-java_11.dmg
+
+codesign --deep -vvvv Jalview_Develop-2_11_2-macos-java_11.dmg
+
+4. Notarize
+xcrun altool --notarize-app --primary-bundle-id "org.jalview.jalview-desktop" -u jalview-dev-owner@jalview.org -p $ALTOOL_PASSWORD --file Jalview_Develop-2_11_2-macos-java_11.dmg
+.. run with --notarization-info $notarization-session-id until complete
+
+5. Staple to dmg so it can be verified without a net connection.
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+ <dict>
+ <key>com.apple.security.app-sandbox</key>
+ <false/>
+ <key>com.apple.security.network.server</key>
+ <true/>
+ <key>com.apple.security.network.client</key>
+ <true/>
+ <key>com.apple.security.files.user-selected.read-write</key>
+ <true/>
+ <key>com.apple.security.cs.allow-jit</key>
+ <true/>
+ <key>com.apple.security.cs.allow-unsigned-executable-memory</key>
+ <true/>
+ <key>com.apple.security.cs.disable-executable-page-protection</key>
+ <true/>
+ <key>com.apple.security.cs.disable-library-validation</key>
+ <true/>
+ <key>com.apple.security.cs.allow-dyld-environment-variables</key>
+ <true/>
+ </dict>
+</plist>
git://source.jalview.org / jalview.git / commitdiff
