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code style & formatters #3

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Merged
brandstaetter merged 11 commits into from
Apr 12, 2013
Merged

code style & formatters #3

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0b11b10
added suggestions for code style
brandstaetter Apr 5, 2013
e0575bf
added suggestions for code style
brandstaetter Apr 5, 2013
250608a
added suggestions for code style
brandstaetter Apr 6, 2013
6b6101f
removing obsolete readme file
andreasprlic Apr 6, 2013
a2581b0
removing eclipse warning
andreasprlic Apr 7, 2013
7f98b99
removing eclipse warning
andreasprlic Apr 7, 2013
9b8c037
cleanup of eclipse warnings
andreasprlic Apr 7, 2013
b57768f
adding checkstyle and findbug plugins to project build
andreasprlic Apr 7, 2013
381d4cd
minor cleanup
andreasprlic Apr 7, 2013
09bd36d
adding gitignore
andreasprlic Apr 7, 2013
ef5d745
Update .gitignore
andreasprlic Apr 7, 2013
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17 changes: 0 additions & 17 deletions biojava3-structure-gui/readme.txt
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This file was deleted.

5 changes: 5 additions & 0 deletions biojava3-structure/.gitignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
/target
.project
.profile
.settings
.classpath
1 change: 0 additions & 1 deletion biojava3-structure/src/main/java/org/biojava/bio/structure/Site.java
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Expand Up @@ -22,7 +22,6 @@

import java.io.Serializable;
import java.util.ArrayList;
import java.util.Formatter;
import java.util.List;
import java.util.Locale;

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3 changes: 3 additions & 0 deletions biojava3-structure/src/main/java/org/biojava/bio/structure/StructureTools.java
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Expand Up @@ -1043,6 +1043,7 @@ private static boolean isHbondDonorAcceptor(Atom atom) {
* @return a structure that contains only the first model
* @since 3.0.5
*/
@SuppressWarnings("deprecation")
public static Structure removeModels(Structure s){
if ( ! s.isNmr())
return s;
Expand All @@ -1055,6 +1056,8 @@ public static Structure removeModels(Structure s){

n.setPDBCode(s.getPDBCode());
n.setName(s.getName());

// we are calling this legacy menthod for backwards compatibility
n.setHeader(s.getHeader());
//TODO: do deep copying of data!
n.setPDBHeader(s.getPDBHeader());
Expand Down
3 changes: 1 addition & 2 deletions ...a3-structure/src/main/java/org/biojava/bio/structure/align/StructureAlignmentFactory.java
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@@ -1,14 +1,12 @@
package org.biojava.bio.structure.align;

import java.lang.reflect.Constructor;
import java.util.ArrayList;
import java.util.List;
import java.util.ListIterator;

import org.biojava.bio.structure.StructureException;
import org.biojava.bio.structure.align.ce.CeCPMain;
import org.biojava.bio.structure.align.ce.CeMain;
import org.biojava.bio.structure.align.ce.OptimalCECPMain;
import org.biojava.bio.structure.align.fatcat.FatCatFlexible;
import org.biojava.bio.structure.align.fatcat.FatCatRigid;
import org.biojava.bio.structure.align.seq.SmithWaterman3Daligner;
Expand Down Expand Up @@ -82,6 +80,7 @@ public static void clearAlgorithms() {
algorithms.clear();
}

@SuppressWarnings("unchecked")
public static StructureAlignment getAlgorithm(String name) throws StructureException{
for ( StructureAlignment algo : algorithms){
if (algo.getAlgorithmName().equalsIgnoreCase(name)) {
Expand Down
24 changes: 11 additions & 13 deletions biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java
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Expand Up @@ -393,8 +393,7 @@ public void setBioAssemblyFallback(boolean bioAssemblyFallback) {
*/

private InputStream getInputStream(String pdbId)
throws IOException
{
throws IOException {

if ( pdbId.length() < 4)
throw new IOException("the provided ID does not look like a PDB ID : " + pdbId);
Expand All @@ -417,7 +416,6 @@ private InputStream getInputStream(String pdbId)
// it probably should be downloaded again...
pdbFile = null;
}

}
if ( pdbFile == null ) {
if (autoFetch){//from here we try our online search
Expand All @@ -440,7 +438,7 @@ private InputStream getInputStream(String pdbId)
}
}
return null ;
}
}

/** Returns null if local PDB file does not exist or should be downloaded again...
*
Expand Down Expand Up @@ -551,7 +549,7 @@ private InputStream getInputStreamBioAssembly(String pdbId)

String fileName = fpath + getBiologicalAsssemblyFileName(pdbId.toLowerCase(), bioAssemblyId);
File f = new File(fileName) ;

// check if bio assembly file exists in local cache
if ( f.exists()) {
InputStreamProvider isp = new InputStreamProvider();
Expand Down Expand Up @@ -733,7 +731,7 @@ private File downloadPDBBiologicalAssembly(String pdbId, String pathOnServer){
// and the fallback has been set, get the original PDB file instead (i.e. for NMR structures).

File f = null;

try {
f = downloadFileIfAvailable(url, pdbId,fileName);
} catch (IOException ioe){
Expand Down Expand Up @@ -783,7 +781,7 @@ private File downloadFileIfAvailable(URL url, String pdbId, String fileName) thr
} else {
tempFile = new File(path + LOCAL_BIO_ASSEMBLY_DIRECTORY + "/" + fileName);
}

return FileDownloadUtils.downloadFileIfAvailable(url, tempFile);
}

Expand Down Expand Up @@ -837,14 +835,14 @@ public boolean checkFileExists(String pdbId){
if ( path != null)
return true;
return false;

}

public void downloadPDB(String pdbId){
//don't overwrite existing files
if ( checkFileExists(pdbId))
return;

if (autoFetch){//from here we try our online search
if(fetchCurrent && !fetchFileEvenIfObsolete) {
String current = PDBStatus.getCurrent(pdbId);
Expand All @@ -860,9 +858,9 @@ public void downloadPDB(String pdbId){
downloadPDB(pdbId, CURRENT_FILES_PATH);
}
}

}


/** load a structure from local file system and return a PDBStructure object

Expand Down Expand Up @@ -1010,7 +1008,7 @@ private String getBiologicalAsssemblyFileName(String pdbId, int biologicalAssemb
return pdbId + ".pdb" + biologicalAssemblyId + ".gz";
}




}
86 changes: 86 additions & 0 deletions development/eclipse/biojava-checkstyle.xml
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@@ -0,0 +1,86 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE module PUBLIC "-//Puppy Crawl//DTD Check Configuration 1.3//EN" "http://www.puppycrawl.com/dtds/configuration_1_3.dtd">

<!--
This configuration file was written by the eclipse-cs plugin configuration editor
-->
<!--
Checkstyle-Configuration: biojava
Description:
Checkstyle configuration that checks the biojava coding conventions.
-->
<module name="Checker">
<property name="severity" value="warning"/>
<module name="TreeWalker">
<module name="JavadocMethod">
<property name="suppressLoadErrors" value="true"/>
</module>
<module name="JavadocType"/>
<module name="JavadocVariable"/>
<module name="JavadocStyle"/>
<module name="ConstantName"/>
<module name="LocalFinalVariableName"/>
<module name="LocalVariableName"/>
<module name="MemberName"/>
<module name="MethodName"/>
<module name="PackageName"/>
<module name="ParameterName"/>
<module name="StaticVariableName"/>
<module name="TypeName"/>
<module name="AvoidStarImport"/>
<module name="IllegalImport"/>
<module name="RedundantImport"/>
<module name="UnusedImports"/>
<module name="MethodLength"/>
<module name="ParameterNumber"/>
<module name="LineLength">
<property name="max" value="120"/>
<property name="tabWidth" value="4"/>
</module>
<module name="EmptyForIteratorPad"/>
<module name="MethodParamPad"/>
<module name="NoWhitespaceAfter"/>
<module name="NoWhitespaceBefore"/>
<module name="OperatorWrap"/>
<module name="ParenPad"/>
<module name="TypecastParenPad"/>
<module name="WhitespaceAfter"/>
<module name="WhitespaceAround"/>
<module name="ModifierOrder"/>
<module name="RedundantModifier"/>
<module name="AvoidNestedBlocks"/>
<module name="EmptyBlock"/>
<module name="LeftCurly"/>
<module name="NeedBraces"/>
<module name="RightCurly"/>
<module name="AvoidInlineConditionals"/>
<module name="EmptyStatement"/>
<module name="EqualsHashCode"/>
<module name="HiddenField"/>
<module name="IllegalInstantiation"/>
<module name="InnerAssignment"/>
<module name="MagicNumber"/>
<module name="MissingSwitchDefault"/>
<module name="RedundantThrows">
<property name="suppressLoadErrors" value="true"/>
</module>
<module name="SimplifyBooleanExpression"/>
<module name="SimplifyBooleanReturn"/>
<module name="DesignForExtension"/>
<module name="FinalClass"/>
<module name="HideUtilityClassConstructor"/>
<module name="InterfaceIsType"/>
<module name="VisibilityModifier"/>
<module name="ArrayTypeStyle"/>
<module name="FinalParameters"/>
<module name="TodoComment"/>
<module name="UpperEll"/>
<module name="OperatorWrap"/>
<module name="OperatorWrap"/>
</module>
<module name="JavadocPackage"/>
<module name="NewlineAtEndOfFile"/>
<module name="Translation"/>
<module name="FileLength"/>
<module name="FileTabCharacter"/>
</module>
56 changes: 56 additions & 0 deletions development/eclipse/biojava-cleanup.xml
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@@ -0,0 +1,56 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<profiles version="2">
<profile kind="CleanUpProfile" name="biojava" version="2">
<setting id="cleanup.remove_unused_private_fields" value="true"/>
<setting id="cleanup.always_use_parentheses_in_expressions" value="false"/>
<setting id="cleanup.never_use_blocks" value="false"/>
<setting id="cleanup.add_missing_deprecated_annotations" value="true"/>
<setting id="cleanup.remove_unused_private_methods" value="true"/>
<setting id="cleanup.convert_to_enhanced_for_loop" value="false"/>
<setting id="cleanup.remove_unnecessary_nls_tags" value="true"/>
<setting id="cleanup.sort_members" value="false"/>
<setting id="cleanup.remove_unused_local_variables" value="false"/>
<setting id="cleanup.remove_unused_private_members" value="false"/>
<setting id="cleanup.never_use_parentheses_in_expressions" value="true"/>
<setting id="cleanup.remove_unnecessary_casts" value="true"/>
<setting id="cleanup.make_parameters_final" value="true"/>
<setting id="cleanup.use_this_for_non_static_field_access" value="true"/>
<setting id="cleanup.use_blocks" value="true"/>
<setting id="cleanup.remove_private_constructors" value="true"/>
<setting id="cleanup.always_use_this_for_non_static_method_access" value="false"/>
<setting id="cleanup.remove_trailing_whitespaces_all" value="true"/>
<setting id="cleanup.always_use_this_for_non_static_field_access" value="false"/>
<setting id="cleanup.use_this_for_non_static_field_access_only_if_necessary" value="true"/>
<setting id="cleanup.add_default_serial_version_id" value="true"/>
<setting id="cleanup.make_type_abstract_if_missing_method" value="false"/>
<setting id="cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class" value="true"/>
<setting id="cleanup.make_variable_declarations_final" value="true"/>
<setting id="cleanup.add_missing_nls_tags" value="false"/>
<setting id="cleanup.format_source_code" value="true"/>
<setting id="cleanup.add_missing_override_annotations" value="true"/>
<setting id="cleanup.qualify_static_method_accesses_with_declaring_class" value="false"/>
<setting id="cleanup.remove_unused_private_types" value="true"/>
<setting id="cleanup.make_local_variable_final" value="true"/>
<setting id="cleanup.add_missing_methods" value="true"/>
<setting id="cleanup.add_missing_override_annotations_interface_methods" value="true"/>
<setting id="cleanup.correct_indentation" value="true"/>
<setting id="cleanup.remove_unused_imports" value="true"/>
<setting id="cleanup.remove_trailing_whitespaces_ignore_empty" value="false"/>
<setting id="cleanup.make_private_fields_final" value="true"/>
<setting id="cleanup.add_generated_serial_version_id" value="false"/>
<setting id="cleanup.organize_imports" value="true"/>
<setting id="cleanup.sort_members_all" value="false"/>
<setting id="cleanup.remove_trailing_whitespaces" value="true"/>
<setting id="cleanup.use_blocks_only_for_return_and_throw" value="false"/>
<setting id="cleanup.use_parentheses_in_expressions" value="false"/>
<setting id="cleanup.add_missing_annotations" value="true"/>
<setting id="cleanup.qualify_static_field_accesses_with_declaring_class" value="false"/>
<setting id="cleanup.use_this_for_non_static_method_access_only_if_necessary" value="true"/>
<setting id="cleanup.use_this_for_non_static_method_access" value="true"/>
<setting id="cleanup.qualify_static_member_accesses_through_instances_with_declaring_class" value="true"/>
<setting id="cleanup.add_serial_version_id" value="true"/>
<setting id="cleanup.always_use_blocks" value="true"/>
<setting id="cleanup.qualify_static_member_accesses_with_declaring_class" value="true"/>
<setting id="cleanup.format_source_code_changes_only" value="false"/>
</profile>
</profiles>
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