/* Begin PBXProject section */
08FB7793FE84155DC02AAC07 /* Project object */ = {
isa = PBXProject;
+ attributes = {
+ BuildIndependentTargetsInParallel = YES;
+ };
buildConfigurationList = 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */;
compatibilityVersion = "Xcode 3.0";
hasScannedForEncodings = 1;
/* End PBXProject section */
/* Begin XCBuildConfiguration section */
- 1DEB919008733D9F0010E9CD /* Debug */ = {
- isa = XCBuildConfiguration;
- buildSettings = {
- COPY_PHASE_STRIP = NO;
- DEBUGGING_SYMBOLS = YES;
- GCC_DYNAMIC_NO_PIC = NO;
- GCC_ENABLE_FIX_AND_CONTINUE = YES;
- GCC_GENERATE_DEBUGGING_SYMBOLS = YES;
- GCC_OPTIMIZATION_LEVEL = 0;
- OPTIMIZATION_CFLAGS = "-O0";
- OTHER_CFLAGS = "";
- OTHER_LDFLAGS = "";
- PRODUCT_NAME = mothur;
- ZERO_LINK = YES;
- };
- name = Debug;
- };
1DEB919108733D9F0010E9CD /* Release */ = {
isa = XCBuildConfiguration;
buildSettings = {
};
name = Release;
};
- 1DEB919408733D9F0010E9CD /* Debug */ = {
- isa = XCBuildConfiguration;
- buildSettings = {
- GCC_WARN_ABOUT_RETURN_TYPE = YES;
- GCC_WARN_UNUSED_VARIABLE = YES;
- PREBINDING = NO;
- SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
- };
- name = Debug;
- };
1DEB919508733D9F0010E9CD /* Release */ = {
isa = XCBuildConfiguration;
buildSettings = {
1DEB918F08733D9F0010E9CD /* Build configuration list for PBXLegacyTarget "mothur" */ = {
isa = XCConfigurationList;
buildConfigurations = (
- 1DEB919008733D9F0010E9CD /* Debug */,
1DEB919108733D9F0010E9CD /* Release */,
);
defaultConfigurationIsVisible = 0;
1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
isa = XCConfigurationList;
buildConfigurations = (
- 1DEB919408733D9F0010E9CD /* Debug */,
1DEB919508733D9F0010E9CD /* Release */,
);
defaultConfigurationIsVisible = 0;
int diff = 0;
int length = 0;
int start = 0;
+ int end = 0;
string seqA = A.getAligned();
string seqB = B.getAligned();
int alignLength = seqA.length();
- for(int i=0; i<alignLength; i++){
- if(seqA[i] != '.' && seqB[i] != '.'){
+ for(int i=0;i<alignLength;i++){
+ if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
start = i;
+ cout << "start: " << start << endl;
+ break;
+ }
+ }
+ for(int i=alignLength-1;i>=0;i--){
+ if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
+ end = i;
+ cout << "end: " << end << endl;
break;
}
}
- for(int i=start;i<alignLength;i++){
+ for(int i=start;i<=end;i++){
if(seqA[i] == '.' || seqB[i] == '.'){
break;
}
*
*/
+
#include "dist.h"
/**************************************************************************************************/
string seqA = A.getAligned();
string seqB = B.getAligned();
int alignLength = seqA.length();
-
+
// this assumes that sequences start and end with '.'s instead of'-'s.
for(int i=0;i<alignLength;i++){
- if(seqA[i] != '.' && seqB[i] != '.'){
+ if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
start = i;
+ cout << "start: " << start << endl;
break;
}
}
for(int i=alignLength-1;i>=0;i--){
- if(seqA[i] != '.' && seqB[i] != '.'){
+ if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
end = i;
+ cout << "end: " << end << endl;
break;
}
}