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Clean up some of the walker help output based on additional experience and 

feedback received.  Also, add a flag to build.xml to disable generation of
docs on demand (use ant -Ddisable.doc=true to disable docs).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2284 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-12-07 21:33:11 +00:00
parent 2cf21317f9
commit d75d3a361a
3 changed files with 110 additions and 17 deletions
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3
build.xml
View File

@ -97,7 +97,8 @@
</target>
<target name="extracthelp" depends="compile"
description="Extract help key/value pair file from the JavaDoc tags.">
description="Extract help key/value pair file from the JavaDoc tags."
unless="disable.help">
<javadoc doclet="org.broadinstitute.sting.utils.help.HelpExtractorDoclet"
docletpath="build"
classpathref="runtime.dependencies"

102
java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -130,31 +130,45 @@ public class CommandLineGATK extends CommandLineExecutable {
// Get the list of walker names from the walker manager.
WalkerManager walkerManager = GATKEngine.getWalkerManager();
Map<String,Collection<Class<? extends Walker>>> walkers = walkerManager.getWalkerNamesByPackage();
// Build a list sorted by walker display name. As this information is collected, keep track of the longest
// package / walker name for later formatting.
SortedSet<HelpEntry> helpText = new TreeSet<HelpEntry>(new HelpEntryComparator());
int longestPackageName = 0;
int longestWalkerName = 0;
for(Map.Entry<String,Collection<Class<? extends Walker>>> walkersByPackage: walkers.entrySet()) {
longestPackageName = Math.max(longestPackageName,walkerManager.getPackageDisplayName(walkersByPackage.getKey()).length());
for(Class<? extends Walker> walkerType: walkersByPackage.getValue())
for(Map.Entry<String,Collection<Class<? extends Walker>>> walkersByPackage: walkerManager.getWalkerNamesByPackage().entrySet()) {
// Get the display name.
String packageName = walkersByPackage.getKey();
String packageDisplayName = walkerManager.getPackageDisplayName(walkersByPackage.getKey());
String packageHelpText = walkerManager.getPackageHelpText(packageName);
// Compute statistics about which names is longest.
longestPackageName = Math.max(longestPackageName,packageDisplayName.length());
SortedSet<HelpEntry> walkersInPackage = new TreeSet<HelpEntry>(new HelpEntryComparator());
for(Class<? extends Walker> walkerType: walkersByPackage.getValue()) {
String walkerName = walkerType.getName();
String walkerDisplayName = walkerManager.getName(walkerType);
String walkerHelpText = walkerManager.getWalkerHelpText(walkerType);
longestWalkerName = Math.max(longestWalkerName,walkerManager.getName(walkerType).length());
walkersInPackage.add(new HelpEntry(walkerName,walkerDisplayName,walkerHelpText));
}
// Dump the walkers into the sorted set.
helpText.add(new HelpEntry(packageName, packageDisplayName,packageHelpText,Collections.unmodifiableSortedSet(walkersInPackage)));
}
final int headerWidth = Math.max(longestPackageName+PACKAGE_INDENT,longestWalkerName+WALKER_INDENT);
// Sort the list of walker names.
walkers = new TreeMap<String,Collection<Class<? extends Walker>>>(walkers);
for(String packageName: walkers.keySet()) {
String packageDisplayName = walkerManager.getPackageDisplayName(packageName);
String packageHelpText = walkerManager.getPackageHelpText(packageName);
printDescriptorLine(formatter,PACKAGE_INDENT,packageDisplayName,headerWidth,FIELD_SEPARATOR,packageHelpText, TextFormattingUtils.DEFAULT_LINE_WIDTH);
for(HelpEntry packageHelp: helpText) {
printDescriptorLine(formatter,PACKAGE_INDENT,packageHelp.displayName,headerWidth,FIELD_SEPARATOR,packageHelp.description,TextFormattingUtils.DEFAULT_LINE_WIDTH);
for(Class<? extends Walker> walkerType: walkers.get(packageName)) {
String walkerName = walkerManager.getName(walkerType);
String walkerHelpText = walkerManager.getWalkerHelpText(walkerType);
printDescriptorLine(formatter,WALKER_INDENT,walkerName,headerWidth,FIELD_SEPARATOR,walkerHelpText, TextFormattingUtils.DEFAULT_LINE_WIDTH);
}
for(HelpEntry walkerHelp: packageHelp.children)
printDescriptorLine(formatter,WALKER_INDENT,walkerHelp.displayName,headerWidth,FIELD_SEPARATOR,walkerHelp.description,TextFormattingUtils.DEFAULT_LINE_WIDTH);
// Print a blank line between sets of walkers.
printDescriptorLine(formatter,0,"",headerWidth,FIELD_SEPARATOR,"", TextFormattingUtils.DEFAULT_LINE_WIDTH);
@ -184,4 +198,62 @@ public class CommandLineGATK extends CommandLineExecutable {
for(int i = 1; i < wordWrappedText.size(); i++)
formatter.format(headerWidthFormatString + "%s%s%n", "", fieldSeparator, wordWrappedText.get(i));
}
}
/**
* Represents a given help entry; contains a display name, a description and optionally some children.
*/
class HelpEntry {
public final String uid;
public final String displayName;
public final String description;
public final SortedSet<HelpEntry> children;
/**
* Create a new help entry with the given display name, description and children.
* @param uid a unique identifier. Usually, the java package.
* @param displayName display name for this help entry.
* @param description description for this help entry.
* @param children children for this help entry.
*/
public HelpEntry(String uid, String displayName, String description, SortedSet<HelpEntry> children) {
this.uid = uid;
this.displayName = displayName;
this.description = description;
this.children = children;
}
/**
* Create a new help entry with the given display name, description and children.
* @param uid a unique identifier. Usually, the java package.
* @param displayName display name for this help entry.
* @param description description for this help entry.
*/
public HelpEntry(String uid, String displayName, String description) {
this(uid,displayName,description,null);
}
}
/**
* Compare two help entries by display name.
*/
class HelpEntryComparator implements Comparator<HelpEntry> {
private static TextFormattingUtils.CaseInsensitiveComparator textComparator = new TextFormattingUtils.CaseInsensitiveComparator();
/**
* Compares the order of lhs to rhs, not taking case into account.
* @param lhs First object to compare.
* @param rhs Second object to compare.
* @return 0 if objects are identical; -1 if lhs is before rhs, 1 if rhs is before lhs. Nulls are treated as after everything else.
*/
public int compare(HelpEntry lhs, HelpEntry rhs) {
if(lhs == null && rhs == null) return 0;
if(lhs == null) return 1;
if(rhs == null) return -1;
return textComparator.compare(lhs.displayName,rhs.displayName);
}
}

22
java/src/org/broadinstitute/sting/utils/TextFormattingUtils.java
View File

@ -2,11 +2,12 @@ package org.broadinstitute.sting.utils;
import java.util.List;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
/**
* Common utilities for dealing with strings.
* Common utilities for dealing with text formatting.
*
* @author mhanna
* @version 0.1
@ -40,4 +41,23 @@ public class TextFormattingUtils {
return wrapped;
}
/**
* Compares two strings independently of case sensitivity.
*/
public static class CaseInsensitiveComparator implements Comparator<String> {
/**
* Compares the order of lhs to rhs, not taking case into account.
* @param lhs First object to compare.
* @param rhs Second object to compare.
* @return 0 if objects are identical; -1 if lhs is before rhs, 1 if rhs is before lhs. Nulls are treated as after everything else.
*/
public int compare(String lhs, String rhs) {
if(lhs == null && rhs == null) return 0;
if(lhs == null) return 1;
if(rhs == null) return -1;
return lhs.toLowerCase().compareTo(rhs.toLowerCase());
}
}
}