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Fixing fatcat -alignPairs #1098

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Merged
josemduarte merged 4 commits into from
Aug 9, 2024
Merged

Fixing fatcat -alignPairs #1098

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28e0d44
Some cleanups
josemduarte Jul 19, 2024
2e8138c
Bringing back alignPairs option, should fix #1096
josemduarte Jul 19, 2024
aeb9379
Merge branch 'refs/heads/master' into issue1096
josemduarte Jul 20, 2024
92ff571
Merge branch 'refs/heads/master' into issue1096
josemduarte Jul 20, 2024
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160 changes: 75 additions & 85 deletions ...ture/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -74,11 +74,10 @@
*
* @author Andreas
* @author Spencer
*
*/
public abstract class AbstractUserArgumentProcessor implements UserArgumentProcessor {

public static String newline = System.getProperty("line.separator");
public static String newline = System.lineSeparator();

protected StartupParameters params ;

Expand Down Expand Up @@ -109,11 +108,6 @@ public void process(String[] argv){

printAboutMe();

// if(argv.length == 0 ) {
// System.out.println(printHelp());
// return;
// }

for (int i = 0 ; i < argv.length; i++){
String arg = argv[i];

Expand Down Expand Up @@ -144,8 +138,6 @@ public void process(String[] argv){

String[] tmp = {arg,value};

//System.out.println(arg + " " + value);

try {

CliTools.configureBean(params, tmp);
Expand Down Expand Up @@ -177,15 +169,17 @@ public void process(String[] argv){
String pdb1 = params.getPdb1();
String file1 = params.getFile1();


try {
if (pdb1 != null || file1 != null){
runPairwise();
return;
}


} catch (ConfigurationException e) {
if ( params.getAlignPairs() != null){
runAlignPairs();
return;
}
} catch (Exception e) {
System.err.println(e.getLocalizedMessage());
System.exit(1); return;
}
Expand All @@ -195,90 +189,103 @@ public void process(String[] argv){
System.exit(1); return;
}

public static void printAboutMe() {
ResourceManager about = ResourceManager.getResourceManager("about");

String version = about.getString("project_version");
String build = about.getString("build");

System.out.println("Protein Comparison Tool " + version + " " + build);
}

private void runAlignPairs() throws ConfigurationException, StructureException, IOException, ClassNotFoundException, InvocationTargetException, NoSuchMethodException, IllegalAccessException {

public static void printAboutMe() {
try {
ResourceManager about = ResourceManager.getResourceManager("about");
String pdbFilePath = params.getPdbFilePath();

String version = about.getString("project_version");
String build = about.getString("build");
if ( pdbFilePath == null || pdbFilePath.equals("")){
UserConfiguration c = new UserConfiguration();
pdbFilePath = c.getPdbFilePath();
System.err.println("You did not specify the -pdbFilePath parameter. Defaulting to "+pdbFilePath+".");
}

System.out.println("Protein Comparison Tool " + version + " " + build);
} catch (Exception e){
e.printStackTrace();
AtomCache cache = new AtomCache(pdbFilePath, pdbFilePath);

String alignPairs = params.getAlignPairs();

if ( alignPairs == null || alignPairs.equals("")) {
throw new ConfigurationException("Please specify -alignPairs!");
}

String outputFile = params.getOutFile();

if ( outputFile == null || outputFile.equals("")){
throw new ConfigurationException("Please specify the mandatory argument -outFile!");
}

runAlignPairs(cache, alignPairs, outputFile);
}

private void runAlignPairs(AtomCache cache, String alignPairs,
String outputFile) {
try {
File f = new File(alignPairs);
private void runAlignPairs(AtomCache cache, String alignPairs, String outputFile) throws IOException, StructureException, ClassNotFoundException, InvocationTargetException, NoSuchMethodException, IllegalAccessException {

BufferedReader is = new BufferedReader (new InputStreamReader(new FileInputStream(f)));
File f = new File(alignPairs);

BufferedWriter out = new BufferedWriter(new FileWriter(outputFile, true));
BufferedReader is = new BufferedReader (new InputStreamReader(new FileInputStream(f)));

StructureAlignment algorithm = getAlgorithm();
BufferedWriter out = new BufferedWriter(new FileWriter(outputFile, true));

String header = "# algorithm:" + algorithm.getAlgorithmName();
out.write(header);
out.write(newline);
StructureAlignment algorithm = getAlgorithm();

out.write("#Legend: " + newline );
String legend = getDbSearchLegend();
out.write(legend + newline );
System.out.println(legend);
String line = null;
while ( (line = is.readLine()) != null){
if ( line.startsWith("#"))
continue;
String header = "# algorithm:" + algorithm.getAlgorithmName();
out.write(header);
out.write(newline);

String[] spl = line.split(" ");
out.write("#Legend: " + newline );
String legend = getDbSearchLegend();
out.write(legend + newline );
System.out.println(legend);
String line = null;
while ( (line = is.readLine()) != null){
if ( line.startsWith("#"))
continue;

if ( spl.length != 2) {
System.err.println("wrongly formattted line. Expected format: 4hhb.A 4hhb.B but found " + line);
continue;
}
String[] spl = line.split(" ");

String pdb1 = spl[0];
String pdb2 = spl[1];
if ( spl.length != 2) {
System.err.println("wrongly formattted line. Expected format: 4hhb.A 4hhb.B but found " + line);
continue;
}

String pdb1 = spl[0];
String pdb2 = spl[1];

Structure structure1 = cache.getStructure(pdb1);
Structure structure2 = cache.getStructure(pdb2);

Atom[] ca1;
Atom[] ca2;
Structure structure1 = cache.getStructure(pdb1);
Structure structure2 = cache.getStructure(pdb2);

Atom[] ca1;
Atom[] ca2;

ca1 = StructureTools.getRepresentativeAtomArray(structure1);
ca2 = StructureTools.getRepresentativeAtomArray(structure2);

Object jparams = getParameters();
ca1 = StructureTools.getRepresentativeAtomArray(structure1);
ca2 = StructureTools.getRepresentativeAtomArray(structure2);

AFPChain afpChain;
Object jparams = getParameters();

afpChain = algorithm.align(ca1, ca2, jparams);
afpChain.setName1(pdb1);
afpChain.setName2(pdb2);
AFPChain afpChain;

String result = getDbSearchResult(afpChain);
out.write(result);
System.out.print(result);
afpChain = algorithm.align(ca1, ca2, jparams);
afpChain.setName1(pdb1);
afpChain.setName2(pdb2);

checkWriteFile(afpChain,ca1,ca2,true);
}
String result = getDbSearchResult(afpChain);
out.write(result);
System.out.print(result);

out.close();
is.close();
} catch(Exception e){
e.printStackTrace();
checkWriteFile(afpChain,ca1,ca2,true);
}

out.close();
is.close();
}


Expand Down Expand Up @@ -411,9 +418,6 @@ private void runPairwise() throws ConfigurationException{

checkWriteFile(afpChain,ca1, ca2, false);




if ( params.isPrintXML()){
String fatcatXML = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
System.out.println(fatcatXML);
Expand All @@ -426,26 +430,12 @@ private void runPairwise() throws ConfigurationException{
System.out.println(afpChain.toCE(ca1, ca2));
}

} catch (IOException e) {
e.printStackTrace();
System.exit(1); return;
} catch (ClassNotFoundException e) {
e.printStackTrace();
System.exit(1); return;
} catch (NoSuchMethodException e) {
e.printStackTrace();
System.exit(1); return;
} catch (InvocationTargetException e) {
e.printStackTrace();
System.exit(1); return;
} catch (IllegalAccessException e) {
e.printStackTrace();
System.exit(1); return;
} catch (StructureException e) {
} catch (IOException | ClassNotFoundException | NoSuchMethodException | InvocationTargetException |
IllegalAccessException | StructureException e) {
e.printStackTrace();
System.exit(1); return;
}
}
}

/**
* check if the result should be written to the local file system
Expand Down
4 changes: 2 additions & 2 deletions ...-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeUserArgumentProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,8 @@
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy;

/** process the arguments from command line
/**
* Process the arguments from command line
*
* @author Andreas Prlic
*
Expand Down Expand Up @@ -154,7 +155,6 @@ public String toString() {
.append(showMenu).append(", printPDB=").append(printPDB)
.append(", isDomainSplit=").append(isDomainSplit)
.append(", alignPairs=").append(alignPairs)
.append(", searchFile=").append(searchFile)
.append(", saveOutputDir=").append(saveOutputDir)
.append(", nrCPU=").append(nrCPU).append("]");
return builder.toString();
Expand Down
49 changes: 15 additions & 34 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/StartupParameters.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,6 @@
* A simple bean that contains the parameters that can get set at startup
*
* @author Andreas Prlic
*
*/
public class StartupParameters {

Expand All @@ -49,7 +48,6 @@ public class StartupParameters {

// for DB searches
String alignPairs;
String searchFile;
String saveOutputDir;
int nrCPU;

Expand All @@ -69,19 +67,8 @@ public StartupParameters(){
nrCPU = 1;
}

/** An input file to be used for the DB search
*
* @return
*/
public String getSearchFile() {
return searchFile;
}
public void setSearchFile(String searchFile) {
this.searchFile = searchFile;
}


/** The file that contains a list of PDB pairs to be aligned
/**
* The file that contains a list of PDB pairs to be aligned
*
* @return
*/
Expand Down Expand Up @@ -109,15 +96,17 @@ public void setShowMenu(boolean showMenu) {
this.showMenu = showMenu;
}

/** Display the output string in CE style
/**
* Display the output string in CE style
*
* @return flag
*/
public boolean isPrintCE() {
return printCE;
}

/** Display the output string in CE style
/**
* Display the output string in CE style
*
* @param printCE a flag
*/
Expand All @@ -129,7 +118,8 @@ public void setPrintCE(boolean printCE) {
public String getPdb1() {
return pdb1;
}
/** mandatory argument to set the first PDB (and optionally chain ID) to be aligned.
/**
* mandatory argument to set the first PDB (and optionally chain ID) to be aligned.
*
* @param pdb1
*/
Expand All @@ -140,7 +130,8 @@ public String getPdb2() {
return pdb2;
}

/** mandatory argument to set the second PDB (and optionally chain ID) to be aligned.
/**
* mandatory argument to set the second PDB (and optionally chain ID) to be aligned.
* @param pdb2
*/
public void setPdb2(String pdb2) {
Expand All @@ -164,7 +155,8 @@ public String getPdbFilePath() {
return pdbFilePath;
}

/** mandatory argument to set the location of PDB files.
/**
* mandatory argument to set the location of PDB files.
*
* @param pdbFilePath
*/
Expand Down Expand Up @@ -232,9 +224,8 @@ public void setFile2(String file2)
this.file2 = file2;
}



/** When writing the results to a file, don;t write as XML but write aligned PDB file
/**
* When writing the results to a file, don;t write as XML but write aligned PDB file
*
* @return flag
*/
Expand All @@ -249,10 +240,6 @@ public void setOutputPDB(boolean printPDB) {
this.printPDB = printPDB;
}





public boolean isDomainSplit() {
return isDomainSplit;
}
Expand All @@ -273,14 +260,8 @@ public String toString() {
+ ", " + newline + " printPDB=" + printPDB
+ ", " + newline + " isDomainSplit="
+ isDomainSplit + ", " + newline + " alignPairs=" + alignPairs
+ ", " + newline + " searchFile=" + searchFile + ", " + newline + " saveOutputDir="
+ ", " + newline + " saveOutputDir="
+ saveOutputDir + ", " + newline + " nrCPU=" + nrCPU + "]";
}







}